Mendelspod Podcast: Recent Episodes
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Mendelspod was founded in 2011 by Theral Timpson and Ayanna Monteverdi to advance life science research, connecting people and ideas. Influenced by the thinking tools developed by Eli Goldgratt, the founders bring a unique approach to media in the life sciences. With help from our advisors around the industry, Mendelspod goes beyond quick sound bites to create a space for probing conversations and deep insight into the topics and trends which shape the industry's future and therefore our future as a species.
Last month Dandelion Health, a healthcare data platform specializing in artificial intelligence and precision analytics, launched a public service to evaluate racial bias in health algorithms. The company is partnered with three major healthcare providers in the U.S. and has access to over 10 million patient records. Anonymizing these records, they then give researchers the ability to test algorithms against patient data to check for bias and equity.
Most of the leaders of genomic medicine that we speak with say we are headed toward genome sequencing at birth. Last year a first-of-its-kind study called the GUARDIAN began piloting just such medicine. The ambitious multi-year study based in New York State is the brainchild of a titan in the field, Wendy Chung.
Ten years ago this week, the Supreme Court unanimously ruled that genes could not be patented.
Today we feature Quantum-SI, one of the new wave of proteomics tools companies. The company was founded by serial life science entrepreneur, Jonathan Rothberg, originally as a long read sequencing company. Though the company pivoted to proteomics, they kept the sequencing part.
It’s a thrilling time to be in proteomics. Today we discuss a recent paper in PLOS One demonstrating how new technology has revealed a novel biomarker for non-small cell lung cancer previously undetected by other methods. The paper could be a model for new proteomics research going forward. Our guests are Margaret Donovan, Product Marketing Manager, and Asim Siddiqui, Senior VP of Research, both at proteomics company, Seer.
SynBioBeta is the largest gathering of the synthetic biology community worldwide. It’s taking place May 23-25 in Oakland, California. John Cumbers is the founder and CEO of the conference, and he joins us to talk about trends in the space and preview this year’s confab.First, we discuss the impact Washington D.C. is having on the field. What doe’s Biden’s love for bio mean for synbio?
Philosophers talk about various kinds of knowledge. There is knowing that something is. We learn that the sun is 90 million miles from the Earth. There is also knowing how to do something. This includes skills we learn like riding a bike or cooking spaghetti. Knowing how is different from knowing that.
Long DNA has arrived. Elegen, a new company based in San Carlos, California, is out this year offering just long DNA. According to their founder and CEO, Matt Hill and today's guest, the company’s product is twenty times more accurate than anything else presently available.What does this mean for the world of biology and the world in general that we're seeing the emergence of a new subindustry devoted specifically to long DNA?
"We’re not a sequencing company," says Molly He, CEO and co-founder of Element Biosciences in our first interview with the leader of the hot new sequencing company which seemed to come out of nowhere this past year. “We’re a biology company.”Not a sequencing company? Element has just taken the lead in the race toward cheap clinical genomes, and their CEO is putting that news aside in today’s interview. Instead, she’s much more interested in touting the company’s core technology “avidity.” The term comes from a core reagent the company has labeled an “avidite.”
Biology is complex, and the life science tool kit continues to expand to meet the challenge of that complexity taking us into the world of multi omics and beyond. Today we talk about 3D genomics and what this additional three-dimensional structural information is telling not just researchers, but clinicians, particularly in oncology.
Today we talk with Simon Fredriksson, CEO and co-founder of Pixelgen Technologies, a company just out of stealth offering spatial technology that maps cellular surface proteins at the single cell level. Called molecular pixelation, the breakthrough technology is designed to first target immune cells.
Editor's Note: Theral's mic malfunctioned in this interview. Fortunately the not as good backup mic did work and John has a good mic. Our apologies.John Greally joins us today. He is the founding Director of the Albert Einstein College of Medicine’s Center for Epigenomics. He’s a pediatrician and a clinical geneticist with appointments in both at Einstein.
Last month the American Society of Human Genetics (ASHG) took a quite remarkable step, putting out a formal statement of apology for its past history of involvement with eugenics. Some say it’s long overdue while some of us didn’t know about this history.
23andMe occupies its own place in the world of genomics. Known for its vision to democratize human genomic information, the company has always gone big and bold, and sometimes controversial. Today we don’t hear much controversy—is that because their approach has won out? In any case, they have certainly achieved a scale that surpasses any other genetic testing company.
Remember all those firsts for synthetic biology that we heard about coming from Craig Venter’s company, Synthetic Genomics in San Diego? The first genome of a whole organism transplanted. First genome synthesized. First synthetic life created.
Oncology has emerged as the most successful disease area for precision medicine. Last year, as the genetic testing industry went through a royal shake-up brought on mostly by external market forces, it's been no surprise that precision oncology has been touted as a core strength. As the industry now works "to be more lean and profitable"--new language one hears these days, cancer testing will be a big part of that effort.
To begin the year, we head across the pond for an outlook on the thriving community of synthetic biology in the United Kingdom.Paul Freemont was a co-author of the UK's synthetic biology roadmap and co-directs SynbiCITE, the national center for the commercialization of synthetic biology. A few years ago the government put an initial investment of $300 million pounds into the field, and "everything was going swimmingly well," says Paul. "Then COVID happened."
Our goal with today’s show was twofold: bring you a practical holiday gift idea and to take you into the world of a synthetic biology entrepreneur. Our guest: Zack Abbott, CEO of ZBiotics.Zack is a scientist turned businessman who is on a mission to change the conversation around GMOs. His first product is a genetically engineered probiotic that alleviates the morning-after hangover by breaking down acetaldehyde. Zack says he chose this product because it’s something consumers can choose to take—unlike a medicine that’s necessary like insulin.
When excitement around early cancer detection first surfaced, we heard about the “pan-cancer” test that would look for any and all cancers, and early. Now that we’re some years into it, the approach is turning out to be more of a narrow one. Which cancer will we likely see targeted first with an FDA cleared test? Colorectal, according to today’s guest.
Winter is here. In America, we're just back from the Thanksgiving holiday when many of us travel and get together. And so far there is no great COVID surge this year. Or is there? Today's guest says there likely is, and we don't know it because of the most significant shift in our pandemic response: at-home testing.
It’s the age of multi omics. Or multi comics, if you don't catch spell check. A few weeks ago at the annual meeting of the American Society for Human Genetics, we were pleased to find not only genomics companies but some proteomics outfits finding a home. As we chatted with one of these, Olink Proteomics, we were blown away to hear that they were announcing the publication of 1,000 scientific papers. It wasn’t so long ago that genomics companies were boasting this kind of milestone. Has proteomics finally achieved scale?
Pharmacogenomic testing, or PGx, is considered low-hanging fruit, a no-brainer for the application of genetic testing in the clinic. And some may think it is small fruit. Not so, says today’s guest, Kristine Ashcraft.
"Currently we lose a life every two minutes in the United States to non-optimized medications,” says Kristine in today’s show. She has spent over twenty years working to see pharmacogenomic testing adopted into standard-of-care medicine. Kristine serves today as the Medical Affairs Director for PGx at the genetic testing company Invitae.
Last week with a crowd of 1,200 customers in a Los Angeles nightclub, sequencing company Pacific Bioscience launched two new sequencers, both long and short read, Revio and Onso. It was a night of great technology, music, and anticipation. Their customers have waited a long time for this moment. Revio offers long read whole genomes at scale for under $1,000.
Last week, during the first International Conference on Newborn Sequencing, a landmark study to sequence the genomes of 100,000 newborns was announced. Called the GUARDIAN study, the project is the brainchild of Wendy Chung, Professor of Pediatrics at Columbia University. The study will take place in New York State and is somewhat similar to an ongoing project in the U.K. being done by Genomics England.
Today spatial biology company, Vizgen, makes their debut on on the program.
When Vizgen CEO Terry Lo was first involved in developing what we now call spatial biology at Perkin Elmer, he admits that he never thought it would have a genomics side to it.
One thinks of Invitae as a leading genetic testing company that has worked to improve clinical quality while bringing prices down. And they are, and they have. But after listening to today's show, you will see that their vision is bigger than that.
Farid Vij is the President and General Manager of Data at Invitae. A year ago Invitae bought a company he co-founded called Ciitizen which was focused on providing patients with access to their complete medical records.
Have you ever heard of proximity ligation? We knew of it in research form back in the day, but not that it had been commercialized until this summer. It’s not every day we come across a powerful new genomics tool on this program. Which begs the question, where have Ivan Liachko and his company, Phase Genomics, been hiding?
The company received a grant this summer from the Bill Gates Foundation as well as the NIH to pursue phage therapeutics. That’s using viruses to go after bacterial infections, particularly those which are developing antibiotic resistance.
Satellite Bio is named descriptively for the way its platform works. Out of stealth in the past few months with what you might call a middle ground approach to generative medicine between stem cell therapy and organ transplant, the company takes its name from the tissue therapy constructs they surgically implant in patients.
A new generation of biologists is pushing the limits of third-generation sequencing, furthering the technology's development and defining new applications to answer biology’s most pressing questions.
This is the express goal for the lab of Vijay Ramani, assistant professor at UCSF in the department of Biophysics and Biochemistry. Vijay also has an appointment in the Institute of Data Science and Biotechnology at the Gladstone Institute, and in 2019 he was named to the Forbes 30 under 30 rising stars in healthcare list.
In our age of specialization, today’s guest, Dr. Will Hwang of Massachusetts General, went against the trend and received three bachelor degrees in different fields.
Or is this the new trend?
Will says that despite the diversity of pursuits, there was a thread that ran throughout his life as a student. He always liked to look at things at the fundamental unit.
While we’re able to sit outside on a warm summer’s night under the ocean of stars, let us contemplate some of the bigger questions. We’re very excited to start out our twelfth season of the podcast with the chemist, Lee Cronin, from the University of Glasgow. Lee published an original and fundamental theory about the universe in the weeks after we taped which has profound implications for the question about the origin of life and could have some interesting applications in genomics.
Arutha Kulasinghe was pumped for the AGBT (Advances in Genome Biology and Technology) Conference this year. He is the Principal Investigator for the Clinical-oMx Lab at the University of Queensland. Dr. Kulasinghe has pioneered spatial transcriptomics using digital spatial profiling approaches in the Asia-Pacific region, contributing to world-first studies for lung, head, and neck cancer and COVID-19. Not gathering last year due to the pandemic, the AGBT conference has became a kind of revival for genome biologists.
Dr. Eric Green has been the Director of the National Human Genome Research Institute (NHGRI) at the National Institutes of Health (NIH) since 2009. Two years ago, he and his colleagues at the Institute came up with a strategic plan for the next ten years. Today we discuss the plan with the director and get his outlook on the future of human genomics.
Dr. Green says human genomics can be roughly divided into four chapters.
There was a tweet thread at the end of the recent Advances in Genome Biology and Technology (AGBT) conference where researchers took a moment of silence for all the sequencing companies that have announced big plans at the conference and then died. It was clearly aimed at this year’s sequencing tools entrant and buzz-generating Ultima Genomics. The company emerged from stealth the week before AGBT announcing the $100 genome with a purse of $600 million backed by funders including Khosla Ventures, Andreessen, and Founders Fund.
Has the pandemic unleashed the molecule of RNA to be the new future of drug development?
Tim Mercer is the Director of the BASE Lab at the University of Queensland which has recently become one of Australia’s leading national facilities for the manufacture and research of RNA technologies. Tim is the next guest in our series on enzymatic DNA synthesis which he says is "a quantum shift” in our ability to synthesize DNA.
Tim then goes on to explore the future of mRNA vaccines and other RNA therapeutics.
Heidi Rehm’s talents for genomics are legendary. Our field has devoured them like a hungry beast.
Discovering an appreciation for the natural logic of genetics in her early school years, Heidi would later learn she was good at the standardization of genomic databases for clinical use. This would make her a pioneering superstar of genomic medicine.
The area of early cancer detection continues to become ever more exciting these days. Each month more companies add liquid biopsies to their product offering as new technologies advance and are able to recognize cancer with increased sensitivity and specificity, particularly from cell-free DNA in the blood.
In a genomics first, Pacific Biosciences has introduced a new method for detecting DNA methylation simultaneously with DNA sequencing. They are calling it 5-base sequencing.
Today on the program, Jonas Korlach, PacBio’s Chief Scientific Officer, and Tomi Pastinen, the Director of the Genomic Medicine Center at Children’s Mercy Research Institute in Kansas City join us to describe the new breakthrough and connect it to clinical possibilities.
Alec Ford is passionate about his message. No wonder. There's an astounding fact in cancer medicine that is little known and could make a big difference. More cancer patients are dying from infections than they are from their cancers. And Alec's company has the technology to do something about it.
One of the underrated but true successes of precision medicine has been pharmacogenomics. Beginning in the ’90s with the approval of the drug Herceptin for HER2 positive breast cancer, tailoring drugs to genotype has been one of the less controversial areas of our field and will only continue to build on the early promise of sequencing the human genome.
Today we talk Michelle Whirl-Carrillo, Director of PharmGKB, a one-stop go-to for pharmacogenomics data that has been funded by the NIH since 2000.
In 1998, in a now-famous paper, molecular biologist Dennis Lo showed that cell-free fetal DNA is present in high concentrations in maternal plasma and serum. The finding has led to an explosive science based on cell free DNA and an industry that we all know as non-invasive prenatal testing. But more and more this science is making itself known in other disease areas, such as cancer, as well.
Specifically, ctDNA is offering higher resolution in cancer treatment.
Today we talk with John Nelson, Senior Principal Scientist at GE Research and veteran in the field of DNA synthesis. On January 7th, 2020, two weeks before the first cases of the coronavirus were reported in the U.S, John and a team of scientists and engineers proposed a new project to DARPA called NOW, or Nucelic Acids on Demand Worldwide. The goal of the project, now fully underway, is to deliver DNA-based vaccines anywhere in the world in three days.
“I’ve seen a lot of revolutions. Now we’re at the beginning of spatial biology, and I think it has the chance to transform life science similar to next gen sequencing, but even more. It’s going to have more ramifications that spread through more disciplines than any of the revolutions I’ve seen in a while.”
Are we now entering the age of proteomics the way we did with genomics thirty years ago?
We were told we should talk to today’s guest by four people in one week. He’s Omid Farokhzad, CEO and Founder of Seer Inc. When we did, we understood why.
Seer offers its customers the chance to “see the proteome in a way that’s never been possible before.” So what does that mean?
"There's an entire field of fragmentomics with a whole lot of people working on it. The DNA which is shed into the bloodstream has a certain length. The length of ctDNA is shorter than cfDNA, and depending on where the cancer cell is located, the fragment size and pattern is different. So you can actually deduce information about the tissue of origin from the fragment length and pattern. And that's just the beginning."
The DNA synthesis space is seeing some real creativity and disruption this past year. One newcomer, in particular, is shaking things up.
Sylvain Gariel is the co-founder and chief operating officer of DNA Script, who has recently launched the world’s first benchtop enzymatic DNA synthesizer. In today's show, Sylvain, co-inventor of the new system, tells how he met his co-inventors at a French gas company and came to invent a whole new way of writing DNA.
Even though Brian McKelligon calls himself a rookie CEO, he comes to the top position at Akoya Biosciences with a veteran’s resume. His path to one of spatial biology’s hottest companies in 2022 worked him up the ranks of some of the top names in life science tools: Affymetrix, Ingenuity, Ion Torrent, and 10X Genomics. Last year Brian led Akoya through an IPO and this year the company has launched a new integrated product line called the Phenocycler-Fusion which they are calling the fastest single-cell spatial biology system on the market.
Harlan Robins is the Chief Scientific Officer at Adaptive Biotechnologies in Seattle. In 2014, Harlan and his brother Chad co-founded Adaptive as a spinout from the Fred Hutchinson Cancer Center where Harlan had served as the head of computational biology. Adaptive has been developing what they call "immune medicine" mainly in the area of cancer. When the corona virus pandemic hit, they came out with the world’s first T cell-based COVID diagnostic. The test has garnered them a lot of data on T cell response to COVID.
“DNA is changing everything for the better,” says today’s guest, Emily Leproust, CEO of Twist Bioscience. Twist has emerged at the heart of what a New York Times Magazine write-up recently headlined The Gene Synthesis Revolution.
Working at the Broad Institute early in his career, Michael Schnall Levin was discovering he was a biologist at heart. He’d begun his studies in physics then done his PhD in mathematics. But he'd wanted “to do math that had an application in the real world.” It was at the Broad that Michael came in contact with the new tools that were revolutionizing biology.
According to scientists, 30,000 species per year are going extinct. That’s 6 an hour, 150 per day. Up to one half of all species could be extinct by 2050.
Chris Mason is back on the program for our end-of-year special. He’s Professor of Genomics, Physiology, and Biophysics at Weill Cornell School of Medicine and the author of such an outstanding book that we had to have him on the program a second time this year.
In a joint interview, Sean George, CEO of diagnostics firm, Invitae, and Christian Henry, CEO of sequencing tools company, Pacific Biosciences, say that “it was clear in the first five minutes of a phone call that they shared a vision for doing something big together.”
What comes through the interview is that this partnership is built on a big vision: speeding up the adoption of whole genome sequencing into clinical medicine as the preferred method for genetic testing.
There are some technologies that become so ubiquitous in biomedical research that their name turns synonymous with their use. This has been the case for the Luminex xMAP platform and multiple biomarker analysis. The product has been applied in just about every area of life sciences including infectious disease, STD, organ transplant rejection, vaccine development, cancer research, immunodeficiency, animal testing, agriculture, and others. (xMAP is a research use only product and not for use in diagnostic procedures.)
DNA is a multibillion-dollar industry in 2021 and satisfies many life science applications, including drugs, reagents, siRNA, PCR, diagnostics, synthetic biology, and many others. Enzymatic DNA synthesis, or EDS, is a new approach to manufacturing DNA that is much more efficient and user-friendly and could disrupt the current market.
If one was going to be a cancer researcher, surely one would want to be Christina Curtis. She’s an associate professor of oncology and genetics at Stanford, and she studies tumor evolution. She’s the Darwin of cancer research.
Because scientists can’t see human tumors evolve in real life, in Christina's lab she creates what she calls "virtual tumors that recapitulate the size and spatial properties of an actual tumor. And evaluating patient data,” she says, "we have found that metastatic seeding could happen very early. That these tumors were born to be bad.”
"Scientists have been putting RNA into cells through a lipid delivery system for 44 years,” says Elie Dolgin. “And that’s ultimately the vaccine that has gone into millions of arms.” Elie is the author of a recent piece in Nature magazine, The Tangled History of mRNA Vaccines. He joins us to talk about his quest to uncover the winding journey that led to the cure that is moving the world forward.
“Why do plants make a host of chemicals they don’t use? One answer that has always intrigued me is that, unlike us, they can’t walk up and walk away from an environment they don’t like. Evolution has honed this space for over 400 million years.”
David Rimm, Professor of Pathology at Yale, was doing spatial biology since before it was called that. He’s known for counting. And he’s been going beyond—beneath?--the model of the cell in biology for years.
Carlo Bifulco joins us today. He’s an Italian who helped persuade one of America’s largest not-for-profit health systems that providing more genomic information to cancer patients early on was the right thing. With 52 hospitals, over 1,000 physician clinics, more than 120,000 caregivers serving communities across seven states—Alaska, California, Montana, New Mexico, Oregon, Texas, and Washington—Providence and Carlo have quite a task ahead. We ask Carlo what is the state of comprehensive genomic profiling at Providence today?
If a company knows genome engineering, that would be Emeryville based Amyris, the Bay Area's crown jewel for synthetic biology. Founded back in 2003, the company first worked on creating biofuels from yeast. Today they have retooled their platform to produce a diversified line of consumer products that have not only rewarded their bottom line but point the world to a model of sustainable consumer goods.
Laura Hercher, host of our sister podcast, The Beagle Has Landed, joins us today to compare notes. Her gig is much more focused on the clinical side of genomics. Genetic counselors are her core audience. Today we do a highlights show looking back over the Beagle's past year.
Chris Mason, Professor of Physiology and Biophysics and prolific genomics researcher at Weill Cornell Medicine, joins us to talk about what he’s doing with the new generation of spatial biology tools. The first papers we dive into are his work on COVID. Chris says the spatial tools have shown us the ravages of the coronavirus on the body like nothing we’ve seen before, i.e. the tissue damage from the cytokine storms and “the long term perturbations such as seeing cells far apart that were usually hanging out together.”
David Steffin is a cancer researcher and physician at Texas Children's whose particular focus is on pediatric cancers. He begins today’s program with some interesting numbers.
"If you go to a scientific meeting, even with the greatest critics, and you ask, how many people in this audience believe that your entire genome will be part of your everyday medical care in fifty years, every person will raise their hand. So the only questions we’re debating are: how do we get there, how soon can we get there, and what evidence base must we have in place before we get there? What’s really exciting to me is getting there sooner rather than later. If we get there 20 years sooner, we are saving thousands of people's lives.”
We’re all aware of the way that next gen sequencing has changed many tests in the clinical laboratory. But some testing has held stubbornly resistant to change. This has been the case in cytogenetics, or the analysis of chromosomes. That is now changing thanks to a technology that is making inroads where next gen sequencing could not.
"We have all of these evidence based tools and evidence based methods, but the problem is it can take upwards of 20 plus years to be truly implemented into care where healthcare providers are using them and patients are receiving them. And this includes medications and diagnostic tools and other types of treatment or screening.”
One of the hottest new trends in biomedical research today is what is known as spatial biology--the ability to capture tissues in a 3D context. It was named Method of the Year by Nature Magazine in 2020. And one of the first automated instruments launched in this market was the GeoMx Digital Spatial Profiler by NanoString. CEO Brad Gray is here to tell us the story of the birth of the DSP and the revolution of 3D biology. What will these new tools enable for the basic and translational researcher?
When Lee Schwartzberg did his training as an oncologist some thirty years ago at Memorial Sloan Kettering in New York, he had a dream. And after training, he set off to make that dream a reality: to bring the resources, expertise, and research that one enjoys at a major research hospital cancer center to the community level.
“The new drug is the engaged individual,” says today’s guest, Daniel Kraft. Daniel is the founder of Exponential Medicine where he has championed digital health and the explosion of wearable technologies. He's also hosting the new Healthy Conversations podcast--go check it out! There you will find interviews with the innovator’s of today’s medical culture, including shows with former FDA Director, Scott Gottlieb, and genomic medicine guru, Eric Topol.
First comes love, then comes marriage; then comes the genomic couple's report. Isn't that how the line goes? Perhaps that's a how it will begin to go. Today's guest is the founder of Orchid Health, which as of this week is offering the world’s first risk prediction couple’s report. Based on whole genome sequencing from a saliva sample that expectant parents take from home, the report will tell them their genetic risk for the major diseases, including brain, heart, cancer, diabetes, and inflammatory bowel.
Will there be a fourth surge of COVID here in the U.S.? Already that we’re asking the question and it’s not an inevitability is a good sign. It’s become a race between vaccination clinics and viral variants.
The U.S. was a bit slow to this race, but we are catching up. Viral surveillance has become a key part of any nation’s pandemic strategy. This past month, PacBio and Labcorp announced a partnership that brings the tool of long read sequencing to this effort.
Kevin Hrusovosky’s career has been dedicated to transforming medicine from reactive “sick care” to preventative personalized care. A serial entrepreneur, he currently serves as the CEO of Quanterix, a company which has just nabbed $700 million and is raising the bar on proteomics testing.
“Genomics can tell you what your predisposition is,” he says in today’s interview, “proteomics can tell you the earliest moment you are in a disease cascade.”
Raj Krishnan has a good story, and probably a good product. More data will tell. He's the CEO of Biological Dynamics, a new liquid biopsy company that is able to detect biomarkers in not only blood but other biological fluids. And the company's products are good for not only cancer but Alzheimer's and other disease areas as well.
Raj comes to precision medicine from electrical engineering. You don't hear that very often. One day in his lab while working on his PhD he had a classic eureka! moment. That unexpected discovery for which every scientist longs.
Mendelspod was live this week at AGBT 2021 where Theral interviewed CEO Erik Holmlin and CMO Alka Chaubey of Bionano Genomics on Tuesday. The topic was the future of big biology.
How fast is the coronavirus mutating? Why is the U.K. variant, or B.1.1.7, more transmissible than original strains of the virus? Is viral surveillance the weak spot in the U.S.'s fight against the pandemic?
It’s been a year since the coronavirus breached American shores. Here to look back with some perspective is New York Times science writer, Carl Zimmer. Carl has authored thirteen books on science, including Planet of Viruses which includes an essay titled, "Predicting the Next Plague."
We’ve all heard of and perhaps worked with data from The Cancer Atlas Project. Now, with the help of new spatial biology tools, researchers at the Mayo Clinic are developing what they call The Cancer Immunome Project. This is a comprehensive effort to fully characterize the immune system and how it interacts with and fights off cancer.
Today we talk with J C Villasboas, a physician-scientist at Mayo who co-started the project. He’s also Director of Mayo’s Immune Monitoring Core Facility.
Has this pandemic presented a unique moment for science in our history? Or is it just a strange and temporary moment of science fiction? Or both? Sci-fi author Kim Stanley Robinson (The Mars Trilogy, The Ministry of the Future) recently penned an essay in the New Yorker about how the virus has “changed our imaginations” and created a new “structure of feeling.”
A discovery here. A paper there. An important paper gets passed over. A fortuitous encounter in a coffee shop among two ambitious scientists. A yogurt company just being a yogurt company. Science moves forward in fits and starts. By the time we read the headline in the paper, “breakthrough of the year,” it can have an inevitable quality about it. Then, in a few years, the historian comes and shows us just how random, messy, and, yes, how beautiful is the business of science.
At the beginning of the year, we were all holding our breath for the future of PacBio. And by all, I mean all. It seems everyone has been rooting for this sequencing technology company.
And why? It’s simple. Pretty much everyone is in agreement that they have the highest quality reads on the market.
We speak directly with the Oracle today. It's Keith Robison, blogger at Omics Omics. Your All Knowingness, we ask, what has happened in the world of sequencing technology this year?
“The companies may need a mulligan,” he quips and laughs.
Our October Review show is a Halloween special this year. Join us around the campfire amidst the sounds of howling wolves as Nathan, Laura, and Count Theracula recall some of their creepiest and spookiest times in the world of genomics.
It's Mendelspod's Haunted House of the Genome.
There’s an urgency about Stephen Kingsmore. Which is not to say he’s in a rush.
He’s the CEO of the Rady’s Children’s Genomics Institute. He and his team have two world records to their name for the incredible speed of diagnosing a rare disease using whole genome sequencing. The latest is 19.5 hours.
Dr. Kingsmore feels they can even shave time off that. They’re shooting for a new record of somewhere around 12 hours.
Diversity’s in the news these days. It's not just political correctness. Let’s look deeper into our field at how limited diversity in genetics is affecting all of us. If you are a member of a minority population and you go into a cancer clinic seeking help, some of the genetic tests on offer may not work for you because of your ethnic background. Not only is this wrong on a social justice level. It turns out it's just bad science.
“In an era where we look at these surveys about trust and everything’s going off the cliff, everyone still trusts the NHS. It’s so deep in the British psyche."
We take a deep dive into a core genomics question that is somewhat philosophical today: “what is a disease, or disability?” This month we heard about a new experimental drug for dwarfism called vosoritide that raised questions for parents of dwarfism. If the drug could make their children taller, would they give it to them? Laura asks “can we put forth a medication for a condition saying those who take it are better off getting rid of it and not be saying those who are not getting it are unacceptable to have these different lives?"
From a career at NIH where he was Chief of the Genetic Disease Branch to academic Chief of Medical Genetics at UCSF to his current business title of Chief Medical Officer at InVitae, Bob Nussbaum has been a central figure in the field of genetic testing. A chief among chiefs. Today he gives our State of Genetic Testing: 2020 Edition.
Our approach is to ask Bob to weigh into the recent debates that have come up this past year. And they can be summarized into one question. Even one word. "Expanded."
Synthetic biology was surging like perhaps no other bio-based industry when the pandemic struck, and it has had some unique weapons in its arsenal for aiding in the fight against COVID. There are the leading vaccine makers such as Moderna using synthetic biology, as well as antibody technology and CRISPR based testing. But many of the surging trends from the last year have only been made more urgent this year: small molecules, food tech, synthetic materials. Living with a pandemic is making humans more aware of our scientific dependence.
First it was all about biomarkers. Then panels of biomarkers. But biology is complicated. Why does one patient respond to an immuno therapy when another which shares the same biomarker does not? Welcome to the age of spatial biology. Garry Nolan joins us today. He's a professor in the Department of Pathology at Stanford who's career has been a journey of seeing intracellular happenings more and more in context. Check out this cool analogy from a new paper his lab put out in Cell.
After a long break, the world's first genomics pundits are back for the season. And they are calm and collected in the face of the strorm on Pennsylvania Ave. We're sixty days from an election. How serious should we be taking politicization of the COVID vaccine, this radical shift on LDTs at the FDA?
We also discuss some regular approvals and on rejection that sent the industry reeling with disappointment. Then it's on to Laura's, Nathan's, and Theral's picks for science of the month.
Welcome back!
We see this new ingredient appearing advertised and in products everywhere. On the billboards, in the new shops next to our favorite restaurant, on the counters at the barbershop and when we pick up our prescriptions at the pharmacy.
C-B-D.
It has to do with the ongoing revolution that’s happening around the country—around the world—regarding the deregulation of marijuana. But there’s another revolution that will change our consumption of cannabinoids. That of synthetic biology.
Mary Norton is a perinatologist and clinical geneticist at UCSF who says that in the age when we are diagnosing ever more rare diseases, adding to the carrier screening panel can be a good thing, but it’s complicated.
But it can be a good thing.
But it’s complicated.
Happy summertime! We had positive news this month about an mRNA vaccine from Moderna. We also saw how during a pandemic, the process of science is especially abnormal. Nathan says let's be happy about the good news. Laura's ringing with alarm bells, sensing conflicts of interest right and left.
Back before the world turned upside down, you know, all those years ago--early this February--a paper popped up on bioRxiv called, “Nanopore adaptive sequencing for mixed samples, whole exome capture and targeted panels." It’s an interesting paper.
In the paper, the authors, led by Matt Loose from the DeepSeq lab at the University of Nottingham, describe a method unique to nanopore sequencing where one can do "selective sequencing of single molecules in real time by individually reversing the voltage across specific nanopores.”
What is the key to getting a coronavirus vaccine? “Manufacturing,” says today’s guest, Jeff Stein of Cidara Therapeutics.
Jeff joined us just last fall to talk about his company’s exciting new technology, an immunotherapy, that is a universal flu preventative and therapy. Yes, you read that right. A universal flu preventative.
Our commentators, Nathan Pearson of Root and Laura Hercher of Sarah Laurence College, join us to look back on month two of the first modern pandemic.
We begin with a scandal that rocked the Twitter science community and talk about how science itself may be having a big moment. Will this be a silver lining for this strange year?
Then it’s on to antibody testing. What would a good antibody test need to do? And will there be tough ethical questions when some “have their immunity papers” and go back to work while others do not?
Why have diagnostic tests for the Coronavirus been slow on the scene? What have been the challenges for lab directors? Were they scientific? Were they regulatory? Were they scaling challenges? Are they still scaling challenges? Supply chain problems?
Elaine Lyon worked for many years at the molecular genetics lab at ARUP at the University of Utah and is now the Clinical Services Lab Director at Hudson Alpha. In both of these jobs she has designed and overseen the design of many diagnostic tests.
After the virus reached American shores, was the FDA quick enough to allow companies and labs to develop their own tests without restrictive oversight? The question sparked a sweeping new bill in congress, the VALID Act that could overhaul FDA oversight of diagnostics altogether—something that has been clamored for for a generation.
Turna Ray has been covering the FDA and diagnostics for GenomeWeb since 2006. She has recently written a piece on the new VALID Act that includes responses from various members of the community.
Laura comes to us from her flat in New York, Nathan is stuck in San Diego, but they are here and ready to discuss what a month ago was a warning and now is a full blown world crisis. What have they faced personally? What are their thoughts on testing? And what are some of their early big picture reactions as to how this will all go down?
We make some time for some Corona-free science as well.
More than one in two hundred people have an inherited form of heart disease. But most don’t know it.
Often on Mendelspod we talk about cancer genomics, but in the area of cardio, too, genetic testing can save lives.
Amy Sturm is the Director of Genomic Counseling and Screening Program at Geisinger Health Systems. There she has led the effort to return the results of cardio genetic tests to over 1,000 patients.
Lisa Alderson has been helping to build genetic testing companies for a while. In 2016 she co-founded her own company, Genome Medical, a tele-genomics firm to help patients and providers understand genetic testing results.
Anyone in the genetic testing industry will know that Genome Medical’s offering addresses a burning need. As Lisa remarks in today’s show, genetics is complicated.
What do we actually know about the novel coronavirus, we ask our two monthly commentators at the outset of February’s review show. Then, speaking of pandemics, as Bernie fever sweeps America, we explore the charge that Medicare for All means an end to innovation.
Laura gives an update on the status of the genetic counseling bill, and Nathan comes to us live from AGBT with highlights from Marco Island.
“To be fully honest, I think some of these tests are scary tests. I’ve had the luxury of testing myself . . . some of this needs to have the physician and the genetic counselor involved.”
That’s Pouria Sanae, a newcomer to our field via Yahoo and Helix. He’s also a Swede which gives him a fresh perspective on American genomic culture. Last month Pouria and his co-founders launched ixlayer, a new platform that integrates many of the players in the genomic medicine space: DTC companies, clinical labs, and physician/providers.
23andMe lays off over 100 employees. Illumina comes to the JP Morgan empty-handed. Has Precision Medicine seen it’s heyday already? Or are we gearing up for another wave of innovation? Nathan and Laura are again ready for the tough questions of genomics.
We begin with the current spat between genetic counselors and the ACMG. Like, . . . huh?
It's our special look back over the entire decade which has Nathan and Laura firing on all fours. Not only do we discover their genomic highlights of the last ten years--ups and downs-- they also pull out their special "future glasses" and come up with a provocative list for the next ten. You don't want to miss this.
But first, we do cover December and that kerfuffle over the George Church dating app. And the genomics of income--really? Did you go for that?
Theral, Nathan, and Laura for an extended broadcast. Happy 2020!
Our end-of-year special guest is one of the U.K.’s top genomicists, Ewan Birney, Co-Director of the European Bioinformatics Institute at EMBL. He is also the non-Executive Director for Genomics England. Ewan's perhaps best known for his work with the ENCODE consortium.
The gene edited babies, Lulu and Nana, turn one. Laura Hercher says it feels like it’s been five years. Nathan says, “Happy Birthday.”
Along with our genomics headline party this month, we also discuss a comment that came in from our last show which leads us to the question, can we discuss science without discussing politics?
It’s Nathan, Laura and Theral for almost a full hour sifting through November’s news.
Just in time for Black Friday, Ancestry.com has launched new health testing. Thanksgiving week (the company calls the shopping holidays the “Turkey Five”) has been kind to what is the largest DNA testing company in the world. Back in 2017, their ancestry test competed with the Instapot for Amazon’s top sellers on the biggest shopping day of the year. To date Ancestry has sold over 15 million DNA tests.
On November 25th, 2018, the world was shocked to find out a Chinese scientist, He Jiankui, had edited the germline of twin girls-and the twins had been born. Many in the scientific community remember that Sunday afternoon well as the story broke on MIT's Tech Review, "EXCLUSIVE: Chinese scientists are creating CRISPR babies."
Today’s guest can even tell you what he had for dinner that Sunday and just what was his reaction. "Holy Shit!"
Warning: the first part of this story can sound quite typical. Three co-founders with backgrounds in genomics and AI found a Stanford spinout. Their goal: to bring the tools of AI and computational modeling to unlock the medical secrets of the genome and deliver those to patients. They call this company, Jungla—Spanish for “jungle”—naming not only their adventure, but the whole problem. Then things get interesting.
In 2013 Twist Bioscience was a newcomer to a market that most of us thought was saturated, cornered, commoditized—that of synthetic DNA. But Emily Leproust and her co-founders saw something different. They saw "a big market with unhappy customers.” Today, with a radically disruptive technology, they are market dominant. Twist is a publicly traded company whose stock has doubled already once since they IPOd last year. Imagine, a DNA synthesis company going public! And then seeing their stock perform so well. This is tricky for the most hyped of tech or biotech startups.
Our Halloween show this year summarizing October’s genomics news has more tricks and treats than spooks and scares. It’s Nathan and Laura back to sift through a big month of happenings from the cool CRISPR upgrade to Inscripta’s bold move in gene editing to Ancestry.com’s shift into health testing.
It’s all here, right now, on Mendelspod.
It’s a hot question in the field today. Recently several studies arguing for increased testing for all breast cancer patients have been published in leading oncology journals.
Peter Beitsch is a breast cancer surgeon in Dallas Texas and co-author of one such study in the Journal of Clinical Oncology. He says that NCCN guidelines were created when tests were much more expensive and in an outdated context and that many patients are going under-diagnosed today.
Not many people have had quite the same view on the genomics revolution as John Stuelpnagel. He co-founded Illumina, Ariosa, and Fabric Genomics (formerly Omicia). And he’s the Chairman of Fabric, 10X Genomics, and Inscripta. And not all had the foresight John did that biology would turn out to be so complex.
John is our guest today to preview and describe what he calls the new “writing” phase of genomics, which he says is already underway.
Ed Abrahams has a message for Nancy Pelosi about HR 3. That’s the new bill in the House to reduce drug pricing.
Ed is the President of the Personalized Medicine Coalition, an advocacy organization in Washington representing our industry which will soon announce a new caucus in congress devoted to personalized medicine. Ed joins us today and says to Pelosi, there’s a better way, a more American way to reduce drug costs.
"Welcome to the era of T2T genomics,” tweeted UCSC’s Karen Miga on August 16th of this year. Then she linked to a paper on bioRxiv that begins:
"After nearly two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. However, no one chromosome has been finished end to end, and hundreds of unresolved gaps persist.”
After the summer break, Nathan and Laura, stir from their beach slumbers, to again offer their anything but sleepy opinions on the latest genomics headlines.
Cathy Smith counts herself among the Gleevec Generation after the landmark targeted cancer therapy. She’s an optimist who believes in the possibilities of precision medicine.
“We are outsmarting cancer,” she says.
Cathy is an Assistant Professor of Hematology/Oncology at UCSF where she is also an MD treating patients. Her area of expertise is in acute myeloid leukemia or AML. She joins us today to discuss a recent group paper and collaboration using new technology to track and monitor cancer evolution at the single cell level.
As another summer winds down, another flu season approaches. Yuuuk. When will we be able to stop living in fear of that crowded plane flight in winter months or waking up congested and wondering . . . dreading, “am I coming down with a cold?”
Yes, we get that annual flu vaccine shot, but each year we still get the bug. Until now, a real universal flu vaccine has eluded drug makers, and having the flu goes on being just part of life. But it doesn't have to be.
Synthetic biology is experiencing a second renaissance and the place to be this October 1-3 is at the SynBioBeta conference in San Francisco. For those of you who are going, today’s show is your preview. For those of you who need a nudge, just listen to what conference founder, John Cumbers, has conjured up in this biggest and most diverse lineup yet.
Some Americans still resist genetic testing for fear they will be discriminated against by insurance companies. Why?
in 2008, Congress passed GINA, the Genetic Information Nondiscrimination Act, to protect us from insurance companies choosing to include us or not for policies based on the genes we came with. Then in 2010, Congress passed the ACA, or Affordable Care Act, and with it protection against preexisting conditions. This includes genetic predispositions.
It’s the kind of plot that makes great science.
There are genes that have been hiding in plain sight, undetected until now. They’ve gone unseen, that is, by short read sequencing. Today’s guest and his colleagues call them “camouflage genes,” and a couple in particular may play functional roles in Alzheimer’s disease.
Mark Ebbert is an Assistant Professor of Neuroscience at the Mayo Clinic where he is using long read sequencing technology and computational biology to study neurodegenerative diseases, including Alzheimer’s and ALS.
We’ve interviewed several CEOs over the years since the Theranos fiasco who avoided any mention of the blighted company whenever the comparison came up. But today’s guest, Murielle Thinard McLane, the CEO of Ontera, jumped at the chance before Theral could get to it.
"Some people might say, well that's the Theranos model. They (Theranos) didn't get it wrong. The demand for a fast, comprehensive point-of-care solution near the patient is there. Where they got it wrong is that you need a technology that is sound to do that!"
If you’re not on the long read sequencing train, you’re not landing in the world of genomics.
A new paper out begins, "Structural variants contribute greater diversity at the nucleotide level between two human genomes than another form of genetic variation.”
The great promise of liquid biopsy technology is in early cancer detection. That is, it's the great future promise. Right? This past month at the annual cancer conference, ASCO, we heard about one such flagship company announcing just which technology they were going to use to do it--DNA methylation.
Nathan and Laura join Theral for our final review show before the summer break. Have you already headed out on vacation? Take us along and stay current with the top stories in genomics.
This month it's gene patents (yes, Congress is really reviving that debate), another gene therapy with another astronomical price tag, and remembering Dr. Henry Lynch of Lynch Syndrome fame.
Those of us watching every shift in the level of adoption of genomic medicine have our eyes closely glued to Geisinger Health System in Pennsylvania.
Adam Buchanan is the Co-Director of Geisinger’s MyCode Genomic Screening and Counseling program, and today we talk to him about the rationale of making genomic screening part of routine medical care.
Our two reigning champions are back for a month packed with news. It’s Nathan Pearson of Root and Laura Hercher of Sarah Laurence College and Host of The Beagle Has Landed Podcast daring to go where no genomics commentators have gone before.
Storylines repeat in genome science every decade or so. The human genome is complete. No. Now it's complete. Or, in the 90's, it was first announced that the first chromosome was sequenced. We have the same story for you today--breaking news from a paper that has not even been published yet: the first “complete” assembly of a human chromosome, end to end, telomere to telomere.
So what’s going on?
"DTC is now too big of an arena to put everything in the same bucket.” This was a line from Laura Hercher, one of our monthly commentators a couple shows back. The statement made its way around Twitter, so we thought we’d have Laura back to the program and ask her to come up with some more buckets. It turns out it’s not that easy. Direct-to-consumer genetic testing is a dynamic and complex space in 2019, a mishmash that quite defies easy categorization.
Today we're joined by Matt Plavan, President of Arcadia Specialty Genomics. The last time we talked with someone from Arcadia Bioscience, a biotech company working on plant genomics in Davis, California, they were confronting GMO regulatory hurdles. Which was a pity. They had created these great new strains of rice and soybeans, among other crops, that were being held from market due to regulations in Southeast Asia. This at a time when world population is . . . well, you know what its doing.
April was a tough month for some genomics companies. The FBI raided the offices of uBiome and two other pioneers in the field failed. Are there broader implications?
Nathan and Laura have returned to first give us some facts and then to throw their hats in the ring.
Lots happened this month in the world of DNA. Tune in and catch it all.
Two years ago Veritas Genetics began offering whole genome sequencing for a thousand dollars. It was a significant milestone—and still is!—not only for what it means about the company providing the genomes but also what it means about the demand for such a product.
There are drug trial failures. And there are drug trial failures.
The recent move by drug giant Biogen to halt their Alzheimer’s drug has not only been a setback for the company—their stock fell precipitously on the news—it’s also been a major setback for the whole research community focused on this disease. The Biogen trial was one of the last of the major drug companies with high hopes for a significant therapeutic step forward for the neurodegenerative disease. The last five years has seen one big pharma players after another throw in the towel.
You order a $99 home DNA test for some holiday pleasure. It’s a bit of fun. Right?
Until it turns your life upside down. Which is when you contact a professional.
From recovering DNA on hundred year old envelopes to bringing it to life from 28,000 year old wooly mammoth samples, it's our genomics version of March Madness. Join Theral, Nathan and Laura for another monthly look back over the headlines.
The history of biomedicine goes something like this:
A new tool is invented. 2. New tool is used in research labs to generate new data and new hypotheses. There is new science. 3. New tool is used in clinical setting to confirm this new science with real patients. 4. Then new tool is adopted into clinical use.
All the buzz these days, single cell DNA analysis instruments have just made it into step three.
"That’s fake news!”
We hear it all the time. And often it is said about scientific facts, for example, recent studies or evidence of global warming. Or the safeness of vaccines. But has the problem with “fake news” been that much of an issue in the life science industry?
Our two favorite commentators are back for our February 2019 month-in-review show, and to give our own twist to Valentine's Day celebrations we take on the topic of family surprises due to DNA testing. This is a phenomenon taking the world by storm in 2019. The Boston Globe had a great headline this past week, "First came the home DNA kits. Now come the support groups."
In 2016, after President Obama announced the Cancer Moonshot in the State of the Union, a very outspoken physician researcher from the Mayo Clinic penned an open letter to Vice President Biden criticizing the project and proposing the money be better spent other ways. It included these lines:
Talk to anyone who’s been around diagnostics or blood sampling for long, and they’ll tell you that nanotechnology is nothing new. Today’s guest, Brett Goldsmith, the Chief Technology Officer at Cardea, says he was involved in the nano revolution that was and then wasn’t 20 years ago. (The older veterans among us might date it back even further, to forty years ago.) So what are Brett and Cardea buzzing about early this year in a new Nature paper?
Nathan and Laura are back for the first time this year for a wild trip past cloned CRISPRd monkeys and the first gene drive in mammals. (Just that?) But first we have to deal with our hangover from the end of last year.
We talk DTC and end with a discussion of the ancient DNA controversy.
You’re a mother, and life is typical. You’re also a pediatrician. Then one day you hear that your daughter is autistic. OK. Then you get the news that, no, it’s not autism but a very rare disease called Sanfilippo Syndrome. From your training as a pediatrician you quickly think back and remember the MPS rare diseases, but nothing else prepares you for what’s ahead.
There are hundreds of pregnancy apps available. So what is unique about the NIH’s new crowdsourcing project called PregSource? “We think PregSource is different because we offer the security and reliability of having been developed at the NIH with the participation of well regarded organizations. We’ve developed the content with expert input at every stage. Their are no ads at PregSource. And, of course, we will never, ever share or sell the data with a commercial organization.”
Today we engage in a rare discussion between a startup founder who is going beyond sequencing and working directly with cancer patient cells in 3D cultures and with one of his customers, the husband of a cancer patient.
Meet Christian Regenbrecht, the CEO of CPO or Cellular Phenomics and Oncology based in Berlin, Germany and Janos Flosser, a fund manager who invests in technology from Copenhagen, Denmark.
It’s the question of the moment Are we living in the age of AI? Or is it still just hype?
When it comes to the latest research in immuno therapy, computational modeling is helping to answer key open questions, such as which patients might respond to which drugs.
"If you were to ask me last year about deep learning, I would probably say, aaah, most of the algorithms that are published are not really answering the important questions yet. But I think this year I am converted. We are starting to use deep learning, and we are starting to see interesting results.”
At the end of the year, we like to speak with a journalist who covers genetics about some of their stories.
Designer babies. The term means many things to many people. To some it means kids only dressed in Gucci.
Some say that by doing pre-implantation genetic screening, we are already living in the age of designer babies. Others have been holding out for that time when humans edit their own germline offering the new progeny not only disease repair, but also enhancements. It's also argued there’s a third category in the middle there somewhere, a protection against disease in the future. That’s what He Jiankui attempted.
A one month old baby is admitted to a hospital with fever. This is cause for serious alarm. The child is put on broad spectrum antibiotics. The infected area is drained and a culture run to try to identify the pathogen. The cultures come back negative, the pathogen not identified.
Sara Radcliffe can be happy--extra happy. She is the CEO of the California Life Sciences Association at a time when the state is breaking records, beating out every other state in category after category. Today Sara discusses a new report the organization has released along with PWC detailing our sector’s explosive growth. Jobs: check. Wages and revenue: check. VC funding: check. NIH funding: check. California leads in all. Big yaaaawn?
What a week! And a great time to have on our expert contributors, genomicist Nathan Pearson and genetic counselor Laura Hercher, to talk about what is reportedly a first in history: babies born with a gene altered. They'll be called Lulu and Nana.
So just how pissed, scared, shocked, and curious are we after three days?
If Mendelspod had an annual Product of the Year award, we'd certainly be liking for 2018 the one featured today, a digital genetic counseling product for direct-to-consumer genetic testing.
Hats are off to Ellen Matloff, a genetic counselor formerly at Yale who saw the DTC boom coming a few years ago, busted out of academia, started My Gene Counsel, and last month launched her first digital product.
The MPS Society is a rare organization. Not just because it is an umbrella for the rare diseases that have in common lysosomal storage malfunction. But because it is one of the largest rare disease organizations in the world.
Terri Klein is the CEO leading the MPS Society. She says the group has over three thousand members on their roster. This brings some strength and resources in an area where low numbers intensifies an uphill battle.
Just hours after Illumina announced their buyout of Pacific Biosciences, Theral sits down with longtime sequencing Omics Omics blogger, Keith Robison, and the Chief Science Officer at sequencing marketplace, AllSeq, Shawn Baker, to discuss the news which has taken the industry by surprise.
A special thanks to our sponsor, Sage Science, and the quick decision on this show.
As an election nears, the question of race and genetics has been front and center. It even prompted ASHG to take the unusual step of making a group wide statement. The three of us agree: scientists should talk more about the race question with non-scientists.
Two papers in Tech Review this month show that the world of people buying cures and disease prevention through gene editing isn’t around the corner, it’s here. Now what about those who can’t afford it? One of the papers was written by our very own Laura Hercher.
Time is health. Take certain blood cancers, for instance. When a patient is seen in a doctor’s office, they are then sent to a central lab for testing, and the results can take a few days. With blood cancer patients, these few days can be vital.
For years a holy grail in diagnostics has been to get diagnostic tests to the point-of-care based on just a few drops of the patient’s blood that could give immediate results.
The title says it all here. Herr Professor Schultze directs a major facility that he calls a single cell genomics platform. They have most of the single cell technologies available and partner with labs from all over the world on research.
Advances in single cell technologies are changing basic research and also delivering results for translational work in everything from immunology to obesity.
“Biology will never be the same again,” says Joachim.
We ran a series this summer highlighting one of the major issues in biomedical research: that the collection, storage, and procurement of biospecimen samples lacks any across-the-board governing standards. Various institutions adopt their own regulations resulting in a checkerboard of quality assurance, and by extension, an unknown effect on the outcomes of research. Our first guest called it “garbage in, garbage out.” (See links below.) This should send shudders through anyone doing research with any human tissue sample.
And here we were thinking it was a slow month!
We have two big stories today: first this philosophy of biology question about whether it’s a bad thing that we’ve been stuck circling the wagons ‘round the same ole genes. Is it just an economic question? Or is it that these are the most active genes, and so we need a meritocracy, as Nathan puts forth?
Vivek Bhalla is used to the question, what’s a nephrologist? When we admitted we’d never had one on the program, he made his own admission, saying that the kinds of people who became nephrologists are the kinds of people who don’t seek out the limelight.
But Vivek, an assistant professor of medicine at Stanford, is changing that and speaking out on behalf of his profession. And he’s very excited about what single cell sequencing has done for the study of the kidney.
She's been a highly sought after venture funder and knowledge broker in the field of digital health. STAT News wrote that upwards of 1,500 pitches crossed her desk last year at GE Ventures. But as of a couple weeks ago, it's a desk at which she's no longer sitting. So what's she up to next?
We like talking to the folks at the Personalized Medicine Coalition (PMC). They have many stakeholders and multifaceted speakers on a wide range of topics. Recently they’re open to talking more about DTC testing—as are most of the traditional diagnostics community. (In our most popular program of the year, CEO of Invitae, Sean George said back in May that the clinical community must “coop” with the rapidly growing DTC movement.)
It’s our first show back after the summer break, and nothing has got us all buzzing about genomics again like a polygenic risk score. It even has Laura Hercher talking about the Human Genome Project doing some delivering, god forbid.
CRISPR has had a rough summer. But still . . . it is CRISPR.
Is Burning Man still cool, we were asked last weekend. Don't know. Don't care. We asked back, is 23andMe still cool?
For the next episode in our summer series on human tissue sample quality and biobanking, we turn to a veteran biobanker in the U.K. who managed several projects there including the U.K. Parkisons’ Disease Society Brain Bank at Imperial College.
Today we talk to Kirstin Goldring, Principal Scientist at Astra Zeneca where she’s in charge of Human Biological Sample Strategy and Governance. Kirstin is a counselor at the European Society for Biopreservation and Biobanking and also a member of ISBER or the International Society for Biorepositories.
As long as we’ve been doing clinical genetics, the goal has been to marry up the genetic data with phenotypic data in the electronic medical records. This has been achieved with some success and with a few of the best genetic markers at some of the leading healthcare providers: Geisinger, Rady Children's, Brigham and Women’s—to name a few. But it hasn’t happened at scale, at least not in this country. Some of the national health services around the world are making the dream more of a reality, for example in Iceland and the U.K.
A book like this only comes around once in a while—one never knows from which corner. This time it was written by the CTO of a next gen sequencing data analytics company.
“Every one of these cases was intense. It was just so fascinating that I had to put it down in a book and tell the story. There’s so much in biology that boggles your mind and makes you wonder.”
When former President Obama’s team released the paperwork for what’s become the All of Us Research Program, in the part about biobanking, the wording specified that the biobanks applying for the grants be “CLIA compliant.”
It seems to be human nature to value and pay up to hundreds of thousands of dollars for a little white pill that we can drop on the floor--and granted, can do wonders for us, but we want to pay nothing or very little to be told what is wrong with us so that we might know which little white pill to use in the first place.
It’s a question we’ve asked on the program before. Are we over relying on the genomics route getting us to biomedical research paradise? Should we be putting more eggs in other baskets?
After combing through lots of clinical trials data, Tony Letai of Dana Farber and the Broad, found that a majority of cancer patients have not benefited from precision medicine. On today’s show he says we need to rethink our approach to cancer research and treatment.
She’s a force of nature, and she’s back on Mendelspod. A decade ago, Carolyn Compton was hired by the NCI to solve a problem that has plagued the world of not just cancer research, but all of biomedical research. To this day, there are no standards in place for the acquisition, collection, storage, and delivery of human biological samples used for research. The leader of the NIH has acknowledged that this is a major part of biology’s non-reproducibility problem.
Nathan Pearson and Laura Hercher are back for a look over a busy month of headlines.
May took us into the era of the free genome as Geisinger planted the genomic medicine flag on an even higher peak. And did you know California was keeping a genetic database for every baby born?
Meh. . . says Laura. Every state does it. Old news.
And mosaicism is old scientific news, says Nathan, but he likes the way Carl Zimmer brings it to light in a new book. Nathan and Laura then go above and beyond with their own elucidation.
If you’ve been in the field of genetic testing then you know about the Greenwood Genetic Center. With an address on Mendel Circle in Greenwood, South Carolina, this non profit diagnostic testing laboratory has basically written the book on diagnosing and understanding genetic disorders. Chances are, too, that you know the director of their cytogenetics lab and our guest today, Alka Chaubey. Her hunger for meeting new people and learning new science is matched only by her desire to share the Greenwood legacy.
You know him, but do you know what he does for a day job?
Over the past two years, Nathan Pearson has dazzled us with his broad knowledge of the genomics space on our regular monthly reviews. Today we’re talking to Nathan about his new company that he soft launched last December, Root Deep Insight, a venture into what he calls “direct-to-lay folk genetics.”
"In a world turned upside down, this is an area where I don’t think he’s had much effect. I don’t think he knows how to spell “DNA.”"
So begins Hank Greely in today’s interview on genetic testing in the age of Trump. Hank is a Professor of Law and, by courtesy, Professor of Genetics at Stanford.
A few years ago they were the new kid on the block, and now they are a leader of mainstream genetic testing. Last year their revenue and profit were significantly up.
And yet in today’s interview, CEO Sean George does not sound like someone sitting back on his laurels. In fact, he says his business model has got to change.
After decades on the loose, it’s cool the cops finally caught him. But is it cool how they caught him?
Nathan Pearson and Laura Hercher are back for April’s headlines. AACR had some more good news about Keytruda, and we take a look at the cancer prediction space.
DNA Day, the first cannabis based therapy to be recommended for FDA approval, the Zuckerberg hearing—there’s lots in here today.
We can all recognize that PacBio has laid down the railroad tracks in the frontier of long read sequencing. What many are asking is just how close on their caboose is Oxford Nanopore? And just what exactly will be the differences between the two technologies?
Chia-Lin Wei is the Director of Genome Technologies at the Jackson Laboratories. When we called her up for today’s interview to talk about how she is using nanopore sequencing, she said, “I’ve been using nanopore for years, why the interest this year by the media?”
Hanlee Ji is the Senior Associate Director of the Stanford Genome Technology Center as well as an oncologist at Stanford. He’s also a clinical geneticist. In other words, he doesn’t need to take off his glasses and spin around in a phone booth to be able to do about everything.
“I was in fellowship for a long time,” he says in todays interview.
23andMe steals the headlines yet again.
“If somebody is worried about breast cancer susceptibility in their family, they should certainly not be using this test.”
That’s our monthly commentator and genetic counselor, Laura Hercher, talking about BRCA going DTC. But wait a minute. Then she says the test could be good in some instances.
“I think the field has just really come to life over the last five or seven years. We’ve got all this sequence data. We’ve got the population data. We’ve got gene editing. I’ve been at this thirty plus years, and we haven’t had a culmination of technology and data like this before. I think everyone has to be excited in some way or other.”
The Personalized Medicine Coalition advocates for a wide group of constituents, including scientists, health care providers, entrepreneurs, payers, and patients. Which is why we’ve often wondered how the organization can be absolutely clear in their priorities.
Today, PMC President Edward Abrahams joins us to answer that question.
"We like to refer to it as consumer initiated, but physician supervised,” says Eric Schadt today when asked if his new test is direct-to-consumer.
Eric is the Dean for Precision Medicine at the Icahn School of Medicine at Mount Sinai in New York and since 2016 has served as CEO of Sema4, a spinoff that he founded out of the Mount Sinai Health System. Sema4 launched a newborn screening panel, Sema4 Natalis, in February of this year covering over 190 disorders.
Booking 26 million viewers, the voice of Warren buffet, the endorsements of Olympians Joey Cheek and Tara Lipinski—this company was going for the gold with their ads during the Olympics this year. Of course, we’re talking of the direct-to-consumer genetic testing company, 23andMe. What was the take of our monthly commentators, Nathan Pearson of Root and Laura Hercher of Sarah Lawrence College?
Also, for all the doomsday predictions, has Donald Trump been any worse after one year for our industry than the biohacker?
Join us for this month’s look back over the headlines.
Sequencing geeks are fresh off the trail from AGBT, and it’s time for our annual look at the sequencing tools space. This year we sit down with the longtime Omics! Omics! blogger, Keith Robison, who not only can answer all your questions about the topic, he even knows which sequencer you’re using right now, and in which department.
Keith jauntily runs through the Big 3--Illumina, Pac-Bio, and Oxford Nanopore--and has a few odds and ends to say about the "niche developers."
Nanopore sequencing has arrived. Passing test after test this past year--including one we discuss today--this technology which was being hyped decades ago is delivering on its promise.
Winston Timp joins us today. He's an assistant professor at Johns Hopkins and one of the leaders on a recent large scale project to directly sequence RNA on an array of nanopores. Winston's is the first in a series of shows we've lined up with users of Oxford Nanopore's technology.
Why RNA-seq? Hasn’t this been done for years?
Some stocks are up on news of big biotech mergers, but others are down on hearing of the latest difficulties of gene therapy. One thing’s for sure—blood diseases are where it’s at.
Speaking of the latest difficulties, we start our January review by going back to that paper out of Stanford about a new obstacle to using CRISPR as a new drug platform. It’s called the human immune system. Major roadblock or small warning light?
Fifteen years ago, folks in the industry were buzzing about RNAi the way they talk about CRISPR today. Then things went quiet for the technology, at least in the news. Until last year.
In September of 2017, Alnylam Pharmaceuticals, the leader in the RNAi space, announced such positive phase III study results that most experts in the business expect an FDA approval soon. It will be the first for an RNAi drug.
A major chapter in the history of medicine has been written by UC San Francisco. They are writing the next for precision medicine.
Reproductive testing is one of the hottest fields in which genetics is going mainstream, a field hurdling us rapidly into the future. It’s an area we’ll be following closely in 2018.
Gary Harton serves as the Chief Operating Officer in the US for Igenomix, a company in the reproductive testing space with a vast global presence. The company has labs in the US, Japan, India, Turkey, Rome, Brazil, Mexico, Canada, and are headquartered in Valencia, Spain.
Our first show of the year is an outlook on genomics for 2018. To do this we’re joined by our regular commentators, Nathan Pearson and Laura Hercher, and also by a special guest to mix things up a bit, Misha Angrist, Associate Professor at Duke University and Editor in Chief of Genome Magazine.
Sharon Begley joins us for our last show of the year to look back over some of the year’s top stories. She’s the senior science writer at STAT News where she covers genetics, cancer, neuroscience and other fields of biomedical research. Prior to joining STAT, Sharon was the senior health and science correspondent at Reuters, the science columnist at the Wall Street Journal, and the science editor at Newsweek.
“I love low tech,” says today’s guest.
It’s not your typical catch phrase for 2017. But then today’s guest is not your typical genome scientist.
A professor in the Department of Chemical Physics at Tel Aviv University in Israel where he runs the NanoBioPhotonix Lab, Yuval Ebenstein came to the genome from an unusual direction. As a physical chemist he started working with DNA as “just a material.”
Our topic today: biotech leadership. What makes a good biotech CEO? Are there unique issues to biotech and diagnostics that shape and demand a different kind of leadership?
It didn’t take long to come up with our lead story for November’s month in review show. Looking at the pictures of the boy in Germany playing soccer after successful treatment of his rare skin disease is just the kind of images we had in mind when we first heard of stem cell therapies.
Carla Grandori was for thirty years a cancer researcher most recently at the Fred Hutch in Seattle. She had her personal reasons for working on cancer, she tells us in today’s show. Now, she’s the CEO and founder of SEngine, a startup offering something completely new for oncologists around the country.
Carla says she was motivated to step out of the research lab when two patients came to her personally and asked her, “can you study my cancer?”
Immuno oncology is now the dominant topic at Mendelspod. From shows with CEOs presenting new panels of predictive biomarker tests, to the firsts at the FDA with the CAR-T approvals as well as the first approval of a drug (Merck’s Keytruda) based on a common biomarker (MSI) rather than on a tumor type, to scientists discussing rare cells of the immune system, we had more podcasts on this topic than any other in 2017.
Here’s a title for you. Chief Genomics Officer. Today’s guest is also the VP of Genomic Medicine and a faculty investigator at the HudsonAlpha Institute for Biotechnology.
The past few months have seen the first approvals at the FDA for CAR-T cancer therapies. But trials have been going on for years. And not just by big pharma.
Today’s guest, Dr. Michael Jensen, is a researcher at Seattle Children’s Hospital and started his first CAR-T cell trial back in 2002.
“It’s been a long road to get to the point where we understand enough about the science and physiology of this technology to make it work int he clinic," he tells us in today's interview.
Modena, Italy is the town where one of the world's rarest cars were first developed and built: the Ferrari sports car. It’s also home to one of the world’s oldest universities where today’s guest spends his time studying rare human cells.
From 1999 to 2013, Deanna Church was a staff scientist at the NCBI where, for a time, she headed the Genome Reference Consortium. This was the effort to continually update, improve and maintain the reference genome. Then Deanna went into private industry, first to Personalis--a genome interpretation company, and now she’s Director of Applications at 10X Genomics--the tools company offering linked read sequencing technology.
If today's guest were a super hero, he'd be High Resolution Sequencing Man.
Bobby Sebra is the Director of Technology Development at the Icahn Institute of Genomics and Multiscale Biology at Mt Sinai in New York. He has the complete arsenal of DNA sequencers in his lab. He specializes in long read applications, and today he goes into several of those spaces, including infectious disease and oncology.
How has sequencing changed since we last had Bobby on a couple years ago, and how does he see it changing in the next two years?
To honor Laura's pentametric thirst, We write the summary today in verse. Was it a quake that had no epicenter, That silly paper out by J. Craig Venter? And after years of silencing the market Has RNAi at last knocked out its target? Then Nathan gives to yuppies devil's choice. Which one libs: gluten dough or GMOs?
We’ve heard a lot this year about the search for new structural variants and the hope that scientists will find new causal linkages for diseases such as cancer. But will the genome still yield dramatic genetic signatures such as KRAS, BRAF and EGFR that have been so helpful in cancer treatment?
Today’s guest says, yes, and he’s on the trail.
When we first talked with Tim Triche of LA Children's Hospital, we found out he was a bit of an outlier among cancer researchers. He was an advocate for poking around in the non-coding RNA.
Today we welcome Tim back to the show to talk about a new gene panel that he has designed specifically for childhood cancers. It’s a first of its kind and was modeled quite closely on the gene panel for the NCI’s MATCH trial. The new panel has both a DNA and an RNA component, and the RNA side is by far the biggest.
Back in 2009, University of Washington professor, Jay Shendure, wrote a definitive paper offering up a roadmap for exome sequencing. Since then, the cost of sequencing has come down so far that many have debated whether or not to do whole genome sequencing vs. just the exome.
Back from summer vacation, Nathan and Laura are smoking hot as they look back over some exciting headlines. The summer boiled over with plenty to talk about, but it was just this week that delivered most of the news for our discussion today. Novartis’ gene therapy based on CAR-T technology was approved Wednesday, making it the first gene therapy to be approved ever in the US. Analysts will be trying to figure out how high high is when it comes to the price tag, but Nathan and Laura explain why this therapy is a big deal for patients.
The challenge for the first ever in-human gene editing trial, according to today’s guest, is with the delivery to the body.
“At the moment, the easiest place to deliver your gene or genome editing is to the liver, using AAV which are viruses that seek out and go to the liver cells," says Sandy Macrae, the CEO of Sangamo Therapeutics.
Sangamo is known for two things: They have pioneered the commercialization of an older gene editing technology called Zinc Fingers. And they have done a lot of work in the area of HIV.
Today we get to bring you a feel good story, one of the major achievements so far in precision oncology. Three large companies—Thermo Fisher, Pfizer, and Novartis—put aside their differences to come together for patients.
The patients are those who suffer from non-small cell lung cancer. In June, the FDA approved for the first time an NGS panel with multiple genes for multiple drugs that treat this kind of cancer.
Invitae appointed their co-founder Sean George as CEO earlier this year. He joins us to share his bold vision for the field of genetic testing.
The life science tools space is flourishing. Biomedical research output is at an all time high. Today’s guest says there are over 40,000 papers published each year on cancer biomarkers.
But very few of those become commercialized tests. Why?
They’re getting a lot of buzz this week. We’re pleased to have Justin Kao, a co-founder of Helix on the program today for the first time.
Barrett Bready is back on the program. He’s the CEO of Nabsys, a company with some new technology for genome mapping.
Originally Nabsys had been working to develop nanopore sequencing, but after a recent reboot has become focused on scaling up scientists' ability to read structural genomic information. Barrett compares Nabsys’ new multiplex technology for genome mapping to the improvement of arrays over single nucleotide (SNP) detection.
George Church joins us today. He’s the Robert Winthrop Professor of . . . . well, he’s George Church. And he confirms that, yes, a movie called “Woolly" is being made about his lab. In the next breath, he reminds us (and himself?) that less than 1% of his press is about the woolly mammoth.
It’s the end of the month--and the half year mark--so we open up today's monthly discussion with Nathan and Laura to include some of the headlines we’ve missed this year.
Last month a paper was published warning about the off target effects when using CRISPR. Laura and Nathan agree the kerfuffle which exploded into this month was more about Wall Street than adding anything new to science.
Remember the technology we used before CRISPR? Sangamo Biosciences launched the first ever “in vivo” (in human) trial for gene editing using Zinc Finger technology.
When will we see the results of microbiome research in our every day lives? And what will that look like?
Rob Knight joins us for the first time today. He’s a professor at UC San Diego and Director of the Center for Microbiome Innovation. He is well known for co-authoring a paper showing that the microbial populations in the guts of obese mice differentiate from those in lean mice.
Reports from ASCO, the nation’s biggest cancer conference, this year again were full of stunning stories about the success of older and new immuno therapies. The race has never been hotter for biomarkers to target patient groups. Most of this new class of drugs--which harnesses the immune system to go after the cancer--inhibit an immune checkpoint called programmed cell death protein 1 or PDL1. So frontline cancer treatment these days typically includes a test for the PDL1 biomarker.
Let’s say you’re a biomedical researcher looking for a place to make your mark. You find out that there is still a major disease that affects more than 2 million people in the US, and we still know virtually nothing about this disease at the molecular level. Wouldn't that stand out?
What does it take to collaborate in genomics?
A platform, for one thing. Over the past few years bioinformaticians have been speculating about a dominant "go to” site that would serve the software needs of those in genomics. Would it be a private company, a Google of genomics? Or would it be a non profit consortium? Would it be created at the government level?
Is Grail already merging? Genomic autopsies? Does the House's new healthcare bill turn mere genetic risk into pre-conditions? Nathan and Laura are back to find meaning in the rush of May's headlines.
Laura cites a disturbing survey of over 2,000 women diagnosed with breast cancer that found half of them had unnecessary double mastectomies after genetic testing. She says unabashedly, “In big letters, it’s an ADVERTSIMENT FOR GENETIC COUNSELING.”
Speaking of alarms, Nathan says attorney Joel Winston’s blog against Ancestry.com’s terms and conditions was fear mongering.
Is health the same thing for an individual as it is for a population? This question goes to the foundation of how we practice medicine today and that of most of genomic research. Michel Accad is a cardiologist in San Francisco and the author of a new book, Moving Mountains: A Socratic Challenge to the Theory and Practice of Population Medicine, in which he uses Socrates to spar with Geoffrey Rose, a British physician and one of the architects of modern medicine.
Mike Snyder is well known in the genomics community for his iPOP (integrated personal omics profiling) study. Profiling himself with hundreds of thousands of measurements each day over a period of seven years and a group of a hundred others for about three years, he and his team at Stanford have shown that sequencing and other omics data can be used to predict Type II diabetes, cancer, heart problems and other disease. He’s also published numerous papers comparing NGS instruments. Now he is expanding iPOP with a whole new set of tools: over the counter wearable devices.
For genomics nerds, April 2017 will be remembered as the date when the FDA adopted a more open policy towards 23andMe and direct-to-consumer (DTC) genetic testing. What does this decision mean, and just where is the FDA drawing the line? A genetic counselor herself, Laura found the decision “head turning.”
“There’s lots of reasons why some genetic counselors are not going to be thrilled to deal with everyone’s 23andMe results,” she says.
Today we follow up with Richard Price, the founder and CEO of the most popular social sharing site for the academic sector, Academia.edu. When we talked to Richard almost five years ago, the site had 1.5 million users, mostly academics sharing their own papers so that their peers had access without any paywalls. Today the site boasts over 50 million users and serves as a laboratory for the future of academic publishing.
Rubbing shoulders at molecular medicine conferences these days one senses a sigh of relief when you talk about laboratory developed tests (LDTs). With the FDA’s decision to put regulation on hold coupled with the expected confirmation of Scott Gottlieb as FDA commissioner, those in the lab testing business seem to be confidently settling back to the status quo. And those who were arguing that all we need is a “beefed up” CLIA to hold labs to better testing standards don’t appear to be motivated to do so anymore.
Talk to someone who attended this year’s AGBT, and you’ll know the big buzz was about single cell genomics. One of the exciting new platforms came from a new player in the genomics space and yet from a very old company.
The largest cut to NIH budget ever, rolling back genetic non-discriminatory law—the bad news continues to roll from Washington. But there was great news this month as well.
Today’s guest makes time to create beauty in the lab. Memo Berkmen is a bacterial artist along with being a staff scientist at New England Bio Labs. He and his colleague, Maria Penil, were the winners of the American Society for Microbiology’s agar art contest in 2015. Their felicitous relationship with the unseen, often unnoticed, world of ancient organisms fills us with wonder and inspiration.
Marc Edwards is telling a different story than the one most of us have been reading and hearing lately. But then he’s used to it.
Marc was the engineer from Virginia Tech who was called one day in September, 2015, by a resident of Flint, Michigan. A Ms Lee Ann Walters wanted Marc to check out her water. When Marc and his team got to Flint they uncovered super high levels of lead in the potable water, with over 100,000 people exposed to high lead levels and 12,000 people with lead poisoning. You know the rest.
Mike Murray and the crew over at Geisinger are making the implementation of genomic medicine look down right easy.
In today’s interview, Mike explains GenomeFIRST Medicine, a program at the Geisinger Health System in Pennsylvania to offer care “that is based on an individual’s DNA sequence.” The healthcare provider boasts its own biobank and has partnered up with Regeneron’s Genome Center to offer exome screening to self selected patients. As of DNA Day last year, April 25th 2016, 100,000 recruits had signed up.
Commentators Nathan Pearson and Laura Hercher join us to look back on February’s genomics headlines.
Beginning this time with science, Nathan says we should be expecting great things from new in-situ sequencing. Laura found it encouraging that the National Academy of Sciences shifted to be more in support of genome editing. Theral asks what life forms are left to sequence for the Earth BioGenome Project?
First of all, watch the video below.
A Santa Cruz company is now previewing a nanopore device that could be a major disruptor in molecular testing. The device is the size of a glucometer and could take all kinds of testing—perhaps someday even cancer-tracking liquid biopsies—into the home with its ease of use and ability to work with thousands of different assays.
Freeman Dyson famously said, “the great advances in science usually result from new tools rather than from new doctrine.”
Today we talk with Mark Fischer-Colbrie, CEO of Labcyte, a company which has made some waves--literally-- in the life sciences by changing a very fundamental laboratory procedure: liquid transfer. For some years now, Labcyte has been selling machines that move liquid around with sound. By eliminating the need for pipette tips and other “solid” surfaces, the machines guarantee much more precision.
Moray Campbell was for all intents and purposes an accomplished and successful cancer biologist at the renowned Roswell Park Cancer Center. Then one day he woke up and realized he was becoming irrelevant. He was a traditionally trained wet lab biologist who was getting left behind by computer science. Any scientist must keep up with their field, but this was different. A few conferences and journals--reading the news everyday was not going to be enough. Facing reality, Moray enrolled in a bioinformatics masters program at Johns Hopkins.
That was in 2013.
Euan Ashley is one of the big names in genomic medicine that has been missing from our guest list. We’re happy to correct that today.
In 2010, he led the team who did the first clinical interpretation of a human genome--that of his Stanford colleague, Steve Quake. Since then Euan, an MD PhD, has been driving to make the use of new genomic tools and discoveries a routine part of medicine at Stanford, particularly in his own discipline of cardiology.
A regular speaker on the conference circuit, Euan titles his talks, "Genomic Medicine Is Here."
As we look back at January’s headlines with our two regular commentators, Nathan and Laura, the question becomes: How much should we ignore the fire raging across America to focus on the science?
Speaking of Trump's new immigration order and the very real threat of a "brain drain," Nathan tells of his own personal time doing research in Iran, commending scientists there and the many Iranian scientists here. But he says Iran has already announced they're going to retaliate.
Why are there no viable psychiatric genetic tests, we ask today’s guest.
Rob Philibert is a geneticist and psychiatrist working at the University of Iowa. He admits at the outset of today’s interview that the field of psychiatric genetics is in a “quandary.”
“The results are not matching the hype,” he says.
Podcast brought to you by: Slone Partners - Providing the leaders that shape the clinical trials space.
About six years ago there was a wave of genome interpretation startups getting their first rounds of funding. One of them was Personalis, a company founded by a well known group of Stanford geneticists and bioinformaticians.
Mark Akeson has been working on nanopore sequencing at UC Santa Cruz’s biophysics lab for twenty years. Up until the past few years with the launch of Oxford Nanopore’s sequencers, that work was mostly the methodical toil of the quiet inventor. Today it is quite ordinary to see a sequencer the size of your wallet being taken out into the field for DNA work. But for years, the naysayers dominated. “Back in the day, the skeptics outnumbered the proponents 99 to 1,” Mark says in today’s show.
Each year at this time, sequencing tools leader, Illumina, generates another round of sequencing buzz in the industry, this year by announcing the $100 genome is around the corner with their latest boxes. But more and more, people are asking just what they will get with that $100. Indeed, what do they get today with a $1,500 genome?
Illumina sells short read sequencing technology which is unable to characterize much of the human genome, particularly complex regions which are responsible for many of the known and unknown diseases.
From new CRISPR trials in humans to mitochondrial transfer therapy, from the spinout by Illumina of two new genomics health companies to the complete and utter failure of Theranos, from the approval by the FDA of GM mosquitos to the FDA giving up on LDT regulation as a result of the election, the genomics headlines of 2016 didn’t fail to dazzle, deliver, and disappoint.
Hear which stories our regular commentators, Laura Hercher and Nathan Pearson, chose as their top and also most underreported of the year in today’s look back on 2016.
Each year at this time we bring on a guest who is somewhat out of the way of our normal lineup, for example, a science fiction writer or a philosopher. Today Theral interviews a law professor who loves to philosophize and write about the impact of biotechnology on our lives now and in the near future. His newest book out this year, “The End of Sex and the Future of Human Reproduction,” is another comprehensive and provocative example of what has made Stanford’s Hank Greely such an in-demand speaker both to scientist and non-scientist audiences alike.
Back in 2009 at the annual AGBT meeting for sequencing, Marco Marra presented one of the first cases of cancer treatment using whole genome sequencing.
We caught up with Marco at his office at the University of British Columbia where he heads the Department of Medical Genetics. Marco also directs the Genome Sciences Center which is part of a very special organization called the BC Cancer Agency.
While everyone is asking what will become of Obamacare, we ask our regular commentators, Nathan Pearson and Laura Hercher, specifically about genomics and medicine.
Nathan begins by saying that data scientists everywhere should be humbled. Does the failure to predict the election send out warnings about big data predictions in genomics?
Today Ethan Perlstein joins us on the program for a third time. His path as a ‘rogue scientist’ has become a bit of a case study here at Mendelspod as we look into alternate paths for scientists and for drug development.
When we talk precision medicine on Mendelspod, we’re usually talking about oncology. But today we shift our focus to diabetes.
Raghu Mirmira is an MD PhD at Indiana University who is working on a panel of biomarkers that would predict Type 1 diabetes. That’s right. Predict.
Having already found a DNA biomarker candidate which detects dying beta cells using the new technology of digital PCR, Raghu is now working to improve the panel with other metabolites.
Let’s take a break from the US and head over to the UK, home of the world’s largest single disease medical research charity. Cancer Research UK (CRUK) raises five hundred million pounds a year for research and drug discovery into any and all of the two hundred plus types of cancer. The charity is extremely well integrated into U.K. culture, and uniquely English in that the donations are mostly small and come from all corners of society. A third of CRUK’s funding comes from donations averaging £10 or less.
Are you lactose tolerant? If you’re of Northern European ancestry this is because of a stretch of DNA in a gene enhancer that developed some 9,000 years ago. That's the same time Northern Europeans began domesticating cattle for milk. If you’re of African ancestry, you may have one of three mutations which appeared independently of the European mutation--and of each other--about 6,000 years ago, again when dairying began.
Today’s show was recorded on Halloween, which now feels so yesterday. Forgive us for some spookiness.
What doesn’t feel so yesterday is the launch this past month of Helix, a company spun out of Illumina that aims to add exomes to the lineup of direct-to-consumer testing. Nathan points out their model for delivering data incrementally through various apps. Laura questions how Helix will vet the apps.
There’s a basic assumption in our field today that has been around for some time. We think of medicine as on a direct and even continuum with science. That discoveries in genomics, for example, will lead directly to breakthroughs in medicine. But the breakthroughs on the medical side have been much more rare to date than those coming from the study of biology and genomics.
As we get closer to the election and the end of 2016, the debate over LDT regulation has gone quiet. At this time last year, there was one hearing after another, first in the Senate, then in the House. The FDA’s Jeffrey Shuren was called before congress and drilled over the nuances of the guidance as well as asked when it would be released. He said, in the first half of 2016.
A couple months back, we reported on a study showing that genetic tests for an inherited heart disorder were more likely to come back with false positive results for black Americans than for whites. The study provoked many in our industry to urge scientists to incorporate more ethnic diversity in their studies. So far, biology has been too Eurocentric—the databases are implicitly racist, they argue.
There were many headlines this past week heralding the first three parent baby to be born. But in fact, as our commentators point out in today’s look back on last month’s genomics news, three parent babies have been around for some time. So why are couples going to Mexico for mitochondrial transfer today? Why is it not legal in the U.S.?
There is tons of life science journalism. Our coffee tables and inboxes fill up each week with that quarterly or that daily. We sift through headlines and product advertisements to assess what’s going on in our industry. It’s our job to know. In this age of several-times-per-day newsletters and 24 hrs a day Twitter, we catch what we can.
And occasionally, we come across a carefully written piece or a well done interview, and we take a moment to realize with some awe the history that is being made in our industry.
Most of the time, when we talk about personalized medicine, it’s not that personalized. What we’re really talking about is population-based medicine. However, there is a growing number of clinical/research groups around the world, including the folks at the Finnish Institute for Molecular Medicine (FIMM) who are combining an older method of functional profiling with new molecular profiling to come up with what the Fins call 'Individualized Systems Medicine.'
The history of science is also a history of toolmaking. And nowhere is this more true than in modern biology. New instruments in the lab allow biologists additional modes of discovery, new levels of quantification, and the opportunity to pursue new and old questions with more data.
For the next installment of our series on genetic counseling, we’re joined by Erica Ramos. She’s the president-elect of the National Society of Genetic Counselors and was the second genetic counselor hired at Illumina where she’s been for four years. Illumina now has 15 genetic counselors.
Erica has been a trail blazer throughout her career. Before joining Illumina, she was the first ‘cancer counselor’ in the city of Las Vegas, Nevada. Her time at Illumina has been a prime example of the evolving role of the industry counselor.
It’s the end of summer and end of another month. Joining us to discuss the genomics headlines of August are Laura Hercher and Nathan Pearson.
A recent study demonstrating that breast cancer patients with low genomic risk may not need chemotherapy is just what precision medicine is all about, isn’t it? Theral and Laura think the study is a big deal. Nathan’s not so sure.
Nathan is convinced though that Eurocentric studies have implicit racism. Laura agrees, saying the lack of racial diversity in biological databases is a major weakness that we must face head on.
Today we feature a pharma company that has been around for some time but recently getting more media coverage for the impressive scale of their new genetic center. Regeneron Pharmaceuticals, insiders joke, has been an overnight success that took 25 years.
One might think every big pharma company has their own genetic center for internal R & D. But today’s guest, Jeff Reid, Executive Director of Genome Informatics at the Regeneron Genetic Center (RGC), says that actually deep genetic research is often outsourced.
We often hear at conferences that there are too few genetic counselors. And that this bottleneck is constraining the delivery and promise of genomic medicine. Is this true?
It is 100% true, says Laura Hercher of Sarah Lawrence College in the second part of our interview on genetic counseling.
“We graduate just under 300 genetic counselors a year. And last year at our annual meeting [National Society of Genetic Counselors], there were posted over 600 jobs. We’re producing jobs at a much greater rate than we’re producing counselors.”
They’ve been called the “unsung heroes” of our age. They are primarily women. And when the trend for most of us is to become specialists, they have been generalists.
Today we begin a special series on genetic counselors. Our first guest, a genetic counselor herself, is a name familiar to our audience. Laura Hercher is one of our regular month-in-reviewers, and today it’s all about her. She is on the faculty at Sarah Lawrence College where the first genetic counseling program was begun in 1969 and where half of the nation’s genetic counselors have been trained.
Today’s show with Jonathan Hirsch, the President and co-founder of Syapse begins a couple years ago. We first featured him on the program in January of 2014 with the headline, Is this the Omics-to-Clinic Site We’ve All Been Waiting For?
On July 6th, as part of the President’s Precision Medicine Initiative, the FDA issued two new draft guidances for the oversight of next gen sequencing (NGS) tests. The first guidance is for using NGS testing to diagnose germline diseases. In the second, the FDA lists guidelines for building and using genetic variant databases.
To help us understand just what the guidance is and what led to its release, we’re joined by Liz Mansfield, the Deputy Office Director for Personalized Medicine at the FDA.
Today's guests have been separately on the program recently. And we've asked them, both Brits, to come back on for a discussion of the Brexit. Clare Turnbull is Clinical Lead for the 100K Genomes Project Cancer Program at Genomics England. Hadyn Parry is the CEO at Oxitec, a company based in Oxford which is already selling their genetically engineered mosquitos into Brazil to deal with viral diseases like Zika and Dengue Fever.
John Carroll has been the editor-in-chief at Fierce Biotech for thirteen years. Now he's moved to a new gig. Two weeks ago, he and a former colleague launched a new and independent life science media site, Endpoints.
Today's show was recorded July 1st, the first day that Vermont’s GMO labeling law went into effect. Just how big a win was this for the anti-GMO crowd, we ask our two commentators, Nathan Pearson and Laura Hercher. They have a surprisingly optimistic take, suggesting that the GMO labeling could become a positive marketing tool.
Kari Stefansson is a name well known in the field of human genetics. His founding of deCODE genetics in his native Iceland in 1996 took our field into a new frontier with the unique opportunity to work with not only a homogenous population but also to integrate with a large centralized healthcare database. It also surfaced a huge ethical debate about genomic privacy.
It’s a non-decision with big implications. On Monday, the Supreme Court turned down an appeal by Sequenom in their patent case with Ariosa. The rebuff by the highest court kills Sequenom’s prenatal screening test patent for good.
You hear it everywhere. And it’s getting old. That "diagnostics is a tough slog.” That it’s the “redheaded stepchild of healthcare.”
And today’s guest doesn’t disappoint, repeating both these phrases. But Brad Gray and NanoString can claim some big “slogging" success. They’re coming out on top in diagnostics through some clever business strategy built on a solid platform. Made CEO at just 33 years of age, Brad has taken NanoString public and overseen a successful expansion from the research to the clinical market.
Today we look back on the genomics headlines over the past month (and a few days). To do this we’re joined by our regular commentators, Nathan Pearson and Laura Hercher.
First we take on the science journalism kerfuffle of the year. When Pulitzer Prize winning author, Siddhartha Mukerjee, got epigenetics wrong in his New Yorker piece, scientists came out en masse to denounce it. Nathan reassures us that scientists aren’t afraid of writers.
Last year when we were promised a soon-to-be-on-the-market, pan cancer, genetic based screening test, many of us were taken aback at the hubris. Not only does the science have a ways to go, there are deep ethical conflicts to work through. However, cancer screening based on a patient’s genetics is already being done in certain niche areas.
There’s been lots in the news this past year about liquid biopsies—those non-invasive tests which locate biomarkers in a vial of blood. Much of that press (perhaps too much) has been about using these blood tests for cancer screening: predictive tests that could be available to consumers some time in the future.
One of the original Celera team that worked on the Human Genome Project, Gene Myers is now setting up the new Center for Systems Biology at the Max Planck Institute of Molecular Cell Biology and Genetics.
However, unlike many others such centers, the main focus of this institute will not be genomics. Rather Myers is going for microscopy.
“Genomics is only about 20% of it,” he says in today’s interview from his office in Dresden, Germany
We’ve heard on the program over the past few years that genomic medicine will probably take off first in a country with a centralized health service. And when the U.K. announced their 100K Genomes Project at the end of 2012 with the creation of Genomics England in 2013, it was certainly a bold visionary move to do just that—to put the entire country on a progressive path toward precision medicine for all.
So with 10K genomes sequenced, how is the project going?
This month we saw Big Money being infused into genomics and other life science research projects. There’s no question that science is big business, but do we see improved healthcare as a result?
Was the NIH too hasty in it’s ban on gene editing of human embryos?
Superheroes are lurking among us everywhere . . . or so the mainstream media would have us believe in their take on a new study from the Icahn School of Medicine.
We hear from some that soon each baby's genome will be sequenced at birth. This vast amount of genomic information will be stored in a person's medical record for life and be referenced for personalized healthcare, be it for a diagnostic, a prognostic, or a prediction. But others say that it is still way too early to be generating so much information on each person when we know so little about the genome. This camp argues that we should deal with patients on a case by case basis using a more targeted approach.
A renewed effort has been underway by leading biologists this year to persuade their colleagues to preprint. This is the posting of a paper to an open access server before peer review and publication. The proponents argue that preprinting will be good for science because discoveries will be made available sooner. The peer review process can take several months, and by preprinting, a biologist doesn’t have to wait to get their work out there and begin interacting with the community.
The promise of rational drug design has driven pharma companies for years. The history of the industry has been one of trial and error, or “guess and check”, as scientists often say. Companies have screened thousands and thousands of compounds looking for one that might work—the proverbial needle in the haystack.
Which company offers the gold standard of sequencing? Nathan starts us out with a metaphor to compare linked reads with real long reads. Then it’s on to this month’s “knockout paper” that moves us yet further from a deterministic view of genetics. Or is this genomic Jenga part of the “proper design of the Creator”? Laura links a new Indiana law banning abortion due to chromosomal abnormalities such as Down Syndrome to a larger effort by the anti-abortion lobby to go after all genetic testing. Theranos plays the Donald Trump of our industry.
Are drug prices really too high? If so, how do we bring them down? Is precision medicine and the use of molecular profiles really making a difference in healthcare today?
These are questions that regularly haunt our industry and the journalists who cover it. But there will be no answers until we face the grand question of all, what today's guest calls the most nagging question in medicine: What is health?
Today we begin a new series focused on just this question.
When 10X Genomics launched their GemCode sequencing instrument at last year’s AGBT conference, what they offered seemed too good to be true. 10X was promising researchers a machine that could generate long reads using Illumina’s short read technology at a price lower than what PacBio could offer with their “real” long read instruments. A year earlier, Illumina had announced they were buying Moleculo, a company that promised to offer long read data out of the short reads. But good data with the Moleculo platform failed to materialize.
Jonas Korlach is a natural storyteller—a rare trait in a scientist who is more comfortable presenting data than talking of himself. Jonas is the co-inventor of PacBio’s SMRT (single molecule, real time) sequencing, and we wanted to hear from him directly how it all got started, and also when the team realized that they had something big with long reads and close to 100X coverage. How many of us can boast of hitting it out of the park on our first try?
It’s the beginning of the age of liquid biopsies, when less invasive, regular blood draws will provide more information than the occasional solid tissue biopsy. Companies that offer tests based on circulating tumor cells or cell free DNA in the blood are popping up like genome interpretation companies were a few years ago. As our understanding of biology at the molecular level advances--particularly in the field of cancer research--the more this practical and focused approach for teasing out the information in the cell, in the body gains steady adoption.
If you attended or followed the recent AGBT conference about all things sequencing, you probably saw a few BioNano Genomics t-shirts with the slogan, “Back to the Map.” They’re referring of course, to a genome map. Just like Google Maps, a genome map consists of landmarks that tell scientists where on the genome they are. But unlike Google Maps and more like the maps North America that were made by European explorers in the 17th century, the map of the human genome is quite incomplete, the map of a frontier.
With constant news topping the headlines about the Zika virus, a synthetic biology company out of Oxford England, Oxitec, has been getting some good press. For over ten years now, Oxitec has been developing their genetically engineered mosquitos as a way to lower virus spreading mosquito populations.
We’re all familiar with the announcement in the year 2000 by US President, Bill Clinton, and the UK’s Prime Minister, Tony Blair, that scientists had completed the first draft of the human genome. It was a big deal. But the actual publications didn’t happen until the next year, February of 2001. Which means that this February is the fifteenth anniversary of the publication of the first human genome. For our commemorative show we’re joined by Mike Hunkapiller, the CEO of Pacific Biosciences.
“It being the month of Hypeuary, go hither through break in yonder wall called LanderGate, and thou wilt be on route to reach the Grail. Drink from this to find your Cure, and Death shall haunt you even more.” -Pithy Monton
OK, so we get it. Long read sequencing technology is cool. But how cool? Is it another great player on the field, or does it change the game altogether?
Pharma companies face escalated flack over high drug prices. Meanwhile the diagnostics industry toils away at comparative pennies to the dollar.
It’s now been over ten years since John Ioannidis published his now famous paper, Why Most Published Research Findings Are False. What response has John seen from the scientific community? How has the paper changed his career and role in the scientific community? Join us for a look at science itself.
As we begin the countdown to the new year, we take a look back at 2015 in cancer research, treatment and prevention. Mendelspod is increasingly becoming known for the coverage of genomics and precision medicine, and cancer as a disease area offers a specific window whereby we can look at practical outcomes.
At the end of the year our goal is to bring the audience some unusual programming, some new outside perspectives on the topics we cover. As with last year, we talk today with science fiction writer, Kim Stanley Robinson, author of the Mars Trilogy, 2312, and Shaman.
We set up an interview with David Spetzler, the CSO of Caris Life Sciences, to hear about some promising new liquid biopsy tests they are developing. And we do that in today’s show. But first, the interview takes a turn toward the regulation of molecular tests. Spetzler says that Caris is already doing as many quality certifications as possible short of FDA oversight.
Angel Pizarro has watched as genomics and cloud computing have grown up together. Formerly a bioinformatics director at University of Pennsylvania, Angel is now the Technical Business Development Manager at Amazon Web Services.
At U Penn, Angel was part of the shift from setting up one’s own facility with expensive computer equipment for handling the rapid growth of omics data to using a third party service, such as AWS. He says that genomics and the cloud are both going through a "second puberty.” In today's show, Angel explains growing pains involved.
In 2004, California voters approved Prop 71 to fund the field of stem cell research by setting up the California Institute of Regenerative Medicine, or CIRM, with $3 billion. George W. Bush was in the White House at the time, and since 2001, his administration had been limiting research that used embryonic stem cells.
We toss the term "precision medicine" around with ease today, and yet payers continue to refuse to pay for diagnostic tests. These are tests that might indicate which treatment will work for a specific patient, thereby saving perhaps hundreds of thousands of dollars, not to mention protecting the patient from unnecessary harm. These are tests which prevent invasive procedures such as unnecessary biopsies.
Josie Briggs is Director of the National Center for Complementary and Integrative Health (NCCIH) at the NIH. She is also currently serving as interim director of the president’s new Precision Medicine Initiative (PMI).
What has happened since the president announced the initiative, what is the proposed timeline going forward, and how much money will there be for the project ongoing?
As the FDA works away on final guidance for regulating LDTs, various professional groups unhappy with the course of the FDA have put together and hurried their own proposals up to Captiol Hill. The Diagnostic Testing Working Group (DTWG) has had their proposal drafted into legislation which has already been revised once in the House Energy and Commerce Committeee, while proposals from the College of American Pathologists (CAP) and the Association of Molecular Pathology (AMP) have been presented to both the Senate and the House.
Here on the show, we’ve talked about the lack of reproducibility for much of biological research. We’ve bandied around various percentages--is it 50% or up to 90% that can't be replicated? And we’ve poked around various issues that may be causing such poor science.
Nicole Perfito is the manager of the Reproducibility Project: Cancer Biology, an effort between Science Exchange and the Center for Open Science. The goal of this project is to take nearly forty “high impact” papers in the field of cancer and try to replicate them.
By listening to him, you wouldn’t know that Peter Maag, the CEO of CareDx, was fighting to keep his company from the brink. We booked Peter for the show after news came out that CMS was once again threatening to lower reimbursement rates of established diagnostic tests.
Today’s story is one of a personal quest, of groundbreaking science, and the creation of a new movement in human genomics.
Jim Lupski is a professor at Baylor College of Medicine where he’s on the frontline of incorporating genomic research into everyday clinical practice. The story begins with Jim’s own genome, which is perhaps the most sequenced genome ever. Jim's life as a leading genomic researcher has been driven in part for a strong personal reason. He has a rare genetic disease named after three researchers who first defined it, Charcot Marie Tooth Neuropathy.
Cliff Reid, CEO of Complete Genomics, is back on the conference circuit, touting a new product. After years of building his company to do sequencing as a service, Cliff presented data at last week's ASHG meeting on Complete's first sequencer as a product, or what they are calling the Revolocity supersequencer.
Cliff was a pioneer in developing the service model, offering only whole human genome sequencing. But after being bought out by BGI, who already had a service business in China, he was compelled to shift his business model to that of selling sequencers.
Earlier this year, the California Life Sciences Association (CLSA) launched, becoming the first statewide policy and advocacy group for biotech. The new nonprofit, a merger between BayBio and the California Healthcare Institute, is led by CEO Sara Radcliffe, former Executive VP of Health at the international Biotechnology Industry Organization (BIO) in Washington.
One of the popular questions on the program this past year is how those doing sequencing decide between the quality of Pacific Bioscience's long reads and the cheaper short read technology, such as that of Illumina or Thermo Fisher. Today’s guest provides the most clear and dramatic answer yet: use the PacBio system exclusively.
K Thomas Pickard is not at all into sports cars. So when he hit midlife crisis, it wasn’t a Porsche or a golf club membership that would reenergize his quiet moments. Nope. K T got his genome sequenced.
The last time we talked with Chris Mason of Weill Cornell Medical College the Supreme Court had just decided the controversial Myriad gene patent case. How forever ago two years can seem. Since then Chris has swabbed and sequenced the microbiome of New York City and began the project of sequencing in space.
His favorite research this year has been to longitudinally profile the genome, epigenome, transcriptome, metabolome and microbiome of identical twins, one in space and one on earth.
Classes for the school year begin this week at Stanford University. New to the faculty is Carolyn Bertozzi, an American chemist who made her name across the bay at Berkeley and was wooed to Stanford by a chance to do research and teach chemistry in a new interdisciplinary institute known as ChEM-H. The institute will bring chemists, engineers, biologists and medical doctors together to understand life at a chemical level. We’ve often heard of biology and engineering institutes, or bringing bio and IT. This institute ups the ante and includes chemistry and medicine.
Though recent guests at Mendelspod say we're not quite to the $1,000 genome, we're close enough to use that benchmark in genomics discussions. But what are we getting for that almost $1,000?
Mark Gerstein is the co-director of the Yale Computational Biology and Bioinformatics program where he focuses on better annotation of the human genome and better ways to mine big genomics data. He has played a big role in some of the large genomics initiatives since the first human genome project, including ENCODE and the 1,000 Genomes Project.
What is a human genome? Well it’s the three billion letters of our DNA. But how is it measured? How do we know when we have it accurately represented?
These are questions that will have to be answered as precision medicine takes hold; for we must have defined standards that will be the basis for regulatory policy, commerce, and better research. These are also the questions that are foremost on the mind of today’s guest.
It's no secret that America's molecular testing laboratories by and large are worried that the FDA's plan to regulate laboratory developed tests, or LDTs, will severely harm patients. Now they have a new proposal which they are taking directly to Capitol Hill. Roger Klein is the Medical Director of Molecular Oncology at the Cleveland Clinic. He’s also serving as the spokesperson for the Association for Molecular Pathology (AMP) on the controversial topic of regulating LDTs.
Diagnostics can be a tough business. The FDA is making a strong push to bring more oversight. Obtaining reimbursement can be outright Sisyphean. And clinicians are slow on the uptake. All of which makes today’s story so good.
The race to the $1,000 genome has been full of breathtaking advances, one after the other. But is next gen sequencing reaching maturity? Will there be that many more significant innovations?
A slow week in life science left us scratching our heads about the purpose of some new studies.
The first, a major project to study the microbes in about 1,200 homes appeared under headlines such as this from Tech Times, "Household Bacteria Can Reveal Volumes about Home Residents." Volumes? Really?
A second study claimed that we are less successful at biomedical research today because life expectancy is not going up at the same rate as the growth in funding or the increasing number of scientists. That's a high bar to set.
It’s taken some time, but the NCI is finally sponsoring a big time clinical trial for cancer where the patients are organized by the genomic pathway that defines their cancer rather than the organ type.
Last week we attended the 2015 Rejuvenation Biotechnology Conference where we heard about the latest developments in aging research.
We were fortunate enough to sit down with two of the major figures in the field of aging research, Aubrey de Grey, CSO of the SENS Research Foundation and Brian Kennedy, CEO of the Buck Institute for Research on Aging. Brian and Aubrey have gone about their work in different ways but say that their approaches are now converging as the momentum behind aging research increases.
We're back in the office after a fabulous vacation, and ready to have some fun. It's Friday, and time for Gene and Tonic.
Yes, we celebrate the news this week that women have their own sex pill. And we make our best guesses as to why the FDA's drug approval rate is up in the stratosphere.
Nathan Pearson, formerly a genome scientist at Ingenuity and Knome, has been doing public outreach for genomics at the New York Genome Center for about a year now. In today’s interview, Nathan says he always wanted to be able to speak directly to the larger public about the great science he’s been involved in.
We recently interviewed cancer researcher Tim Triche from Children's Hospital Los Angeles. Tim had two main points: First, microarrays are still a very valuable tool for research and for the clinic. Second, there are perhaps more answers for cancer research to be found in the non-coding portion of the genome than in the genes. Here, we've compiled Tim's comments on the staying power of arrays.
Major outbreaks of deadly viruses, such as the recent spread of Ebola in Northern Africa, are nothing new on planet earth. What is new is the technology that we are using to identify, track, and contain such plagues.
Emmanuel Vincent is the founder of Climate Feedback, a project which includes a new tool for scientists to comment directly on climate science news. The tool is a plugin which can be downloaded for free and gives a viewer real time access to the feedback of scientists on a particular online article.
Matt Might came knocking on the door of genomic medicine out of pure necessity. After a four year diagnostic odyssey that led them to Duke University, Matt and his wife, Cristina, finally found out through exome sequencing that their son, Bertrand, was suffering from a rare disease known as NGLY1 deficiency. That was three years ago.
Last year, pharma giant Roche went on a buying spree, picking up one company after another. In December, when it was announced they had bought out Bina Technologies, many of us were playing catch up. Who is Bina, and how do they fit in the overall bioinformatics space?
In the second part of our interview with Tim Triche, Director of the Personalized Medicine Center at Children’s Hospital Los Angeles, Tim says that micro arrays are still a vital technology for today’s cancer researcher. Making use of both next-gen sequencing and arrays for his research, Tim confirms that arrays still have advantages in the clinic as well, such as quicker turn around time. Tim also weighs in on some ongoing questions about whether poor biospecimen quality is hampering research efforts and whether genomic medicine is paying off for patients.
Listen to Tim Triche from Children's Hospital Los Angeles for very long and you’ll get excited again about cancer research. I couldn’t stop listening. Which is why his interview is being published in two parts. Now sure, like other guests we’ve had on the show, Tim calls this the “absolute golden age of biomedical research.” But Tim has a unique story. He has been, and is still - though less so now, he says - an outlier in cancer genomics. Whereas most cancer researchers talk about genes, Tim is more interested in non-coding RNA.
When science journalist Ivan Oransky co-founded Retraction Watch, a blog with the express purpose of making scientific retractions more public, he didn’t think he would be posting much. “Adam Marcus, my co-founder, was quoted as saying, ‘yeah, we figured we’d post periodically, our mothers would read it, they’d be very happy, nobody would read it other than them.’ Obviously that hasn’t been the case,” says Oransky in this first of a series of podcasts on scientific integrity.
What a week for Americans . . . What a week for genomics! The Supreme Court rulings that Americans can keep their Obamacare and can all get married - no matter what state they live in - added the final good news to a week of genomics festivities around the country. But it's not all positive news this week. The New York Times featured a diagnostics company under review by Medicare for fraud. Allegedly, the New Orleans based Renaissance Rx has been paying doctors to sign up patients for a huge trial of genomic based tests, even when the patients didn't qualify.
Art Caplan is a prodigious writer on the topic of medical ethics. How prodigious? How about thirty-two books and over 700 peer reviewed papers on ethical conundrums ranging from organ donation to end of life care.
The international BIO convention is all about seduction. All fifty states sent representatives to Philly this week to make the case that their state was the best for biotech. Seventy countries were there touting their awesome awesomeness. Does all this seduction really work? A new class of drugs for cardiovascular disease was reviewed recently at the FDA. Will they become blockbusters like Pfizer’s Lipitor?
Before Bobby Sebra became the Director of Technology Development at the Icahn School of Medicine at Mt Sinai in New York he worked at Pacific Biosciences, helping to develop their single molecule, long read (SMRT) sequencing technology.
It’s a week of finding out again what we already knew. First that a nobel laureate can also be a total ***hole. And second that creative people really are crazy.
It’s also been a week for going into the future. This week Team Mendelspod attended IndieBio’s Demo Day. Twelve, mostly very young, founder/geeks pitched their new ideas for making the world a better place to a room of investors in downtown San Francisco. We saw some amazing technology, but the real question seems to be, how will they sell these new synthetic biology products?!?.
Gene and Tonic for June 5, 2015 What does genomics have to do with a hippie rock music event? A few things. Find out in today’s humorous preview of the Festival of Genomics, happening later this month in Boston. Yes, there are the sports genes everyone knows about. But what about those less studied that might affect your career in sports? Do you know what is written on the sports page of your genome? And what has Ben Carson considering brain surgery? Tune in to this week’s wrap of genomics news - it’s another Gene and Tonic from Mendelspod.
Jeremy Koenig is a molecular biologist and an athlete. His interest in both led him to found a new direct-to-consumer genetic testing company called Athletigen.
If you haven’t already, check out the inaugural Festival of Genomics being held in Boston later this month.
Gene and Tonic: May 29, 2015 Did you hear? The Age of Genomics has come to an end. According to science journalist, David Dobbs, after 110 years of studying genomics, we have come up with almost nothing to improve human health, or as Dobbs put it so elegantly, we ain't got "diddly-squat." What will all of our geneticist friends do? They don't want to be known as "diddlly-squaticists."
By 2050, there will be 9 billion people on the planet. What will they eat? This is the question that led Rod Wing, Director of the Arizona Genomics Institute, into the field of plant genomics. What has been accomplished so far in the mission to come up with some super green crops? And how does Rod see anti-GMO sentiment and the recent trend toward gluten free diets factoring in?
A very unique biotechnology event took place this week.
BEINGS 2015, or the Biotech and the Ethical Imagination Global Summit, was held at The Tabernacle, a former church turned concert hall in Atlanta, Georgia. The venue was not the only unusual thing for a summit about science. Speakers at the meeting included a well known linguist, a famous Canadian novelist, and Catholic rector along with professors of bioethics, law, and, of course, biology.
If you followed the news from the recent show of the American Association for Cancer Research (AACR), no doubt you heard about the exciting potential of liquid biopsies. These new blood-based tests, made possible by better tools and analysis techniques, offer a non-invasive way of understanding various cancers. Traditionally, with non-hematological cancers, solid tumor biopsies are obtained through surgical recession or an invasive needle.
In a keynote talk this week for the online Genetics and Genomics conference, computational biology whiz, John Quackenbush, listed some pretty wild correlations found by a Harvard Business School student when he mixed some large data sets. For example, U.S. spending on science, space, and technology corresponds directly with suicides by hanging, strangulation and suffocation. We never would have guessed it without the help of big data.
Just as biomedical research is experiencing a surge of translation into clinical application, so too must the stories of this research and its impact in the lives of patients be translated to a larger audience.
The New Republic argued in a pice entitled, "The Decline of Pseudoscience," this week that now that the so called "natural" living industry has gone mainstream, "it's days are numbered." Surely Oprah's dumping of Dr. Oz backs this up. But other events this week show a different story.
Janitors have had a terribly busy time this week cleaning up all those jaws that were dropped on floors of research labs everywhere around the country. Have you heard about this latest sexism scandal? Two female co-authors of a scientific paper submitted their work to PLOS -- you know, the open access journal. You won’t believe what they heard back from the lone peer reviewer. They were told to go find “one or two male biologists” to be co-authors on the paper to increase its chances of being published.
Pharma companies have always had their chief medical officers (CMOs). Now, as the diagnostics industry grows, many kinds of life science companies are filling this important position as well. Sequencing tool makers, direct-to-consumer firms, bioinformatics companies—they’re all appointing CMOs.
An Old New DTC Co. on the Move Let’s start with a bit of trivia. What company has resorted to selling genetic ancestry testing online direct to consumers? Hint: the company is located in the San Francisco Bay area, has banked more than 800,000 samples from customers all over the world, and is slowly transforming itself into major biomedical player. That’s right. You got it. It’s Ancestry.com.
When President Bill Clinton stood with Francis Collins and Craig Venter in 2001 to announce the sequencing of the genome, the genome wasn’t really done.
Actually there was no news this week. It turns out the whole industry took the week off to watch the stunning Ken Burns documentary on cancer. No, that’s not true. We did find some news. How about this? The Affordable Care Act turned five this past week. Happy Birthday, ObamaCare! So we thought we’d share some important numbers about the ACA: 11.7 million: the number of Americans who have signed up for 2015 coverage. 46%: the increase in enrollment from 2014 to 2015.
Will tech companies like Google and Apple be good at life science applications? We pursue this question today with Dale Yuzuki, the avid life science blogger, scientist, and now a marketing manager at Thermo Fisher. (See his recent blog, The Core Competency of Google Is Not Life Sciences.)
The future of diagnostics is in the hands of those taking care of the biospecimen samples says, Andy Brooks our final guest in the series, Improving Biospecimen Standards. Andy is the Chief Operating Officer at Rutgers University Cell and DNA Repository, or RUCDR.
More than with any other major disease, the understanding and treatment of cancer is being transformed by genomics. And these are early days.
John McPherson has been involved in sequencing since the original Human Genome Project. He now directs the Genome Technologies Program at the Ontario Institute for Cancer Research. John chaired a panel on cancer genomics at the recent AGBT, or Advances in Genome Biology and Technology conference, and shares his thoughts on this year's meeting.
Friday March 13th
It’s Friday already and time for Gene and Tonic, our wrap of the week’s headlines.
On Monday, Apple’s CEO, Tim Cook, announced that the iWatch is indeed a reality. The iWatch has all the wearable techies and mobile health folks doing somersaults. But it was what happened afterward that was so interesting. Did you hear about this?
Direct-to-consumer (DTC) genetic testing has had a bumpy ride.
Back in 2010, Pathway Genomics and Walgreens made a deal to sell DTC genetic tests in thousands of Walgreens drugstores. Within 48 hours of the deal being announced, it collapsed. The FDA sent a letter to Pathway basically asking them what the hell they were doing. Walgreens quickly elected to put the kibosh on the partnership.
Go about anywhere in the life science industry, and you’ll run into someone who once worked at Affymetrix. Since the founding of Affymetrix and the development of what’s come to be known simply as the Affy chip, the company’s history has been intertwined with that of biotech and the genomics revolution. But what has become of the company today?
Join Theral for a quick wrap-up of the week's biotech news:
The biggest news this week has been the flow of stories coming from last week’s AGBT conference held in Florida. This is the annual all out party for the all out darling of our industry, the sequencing space. Like a debutante ball, it’s where anybody who’s anybody comes out and does their curtsy to society.
Keira Havens is the co-founder of Revolution Bioengineering, and this week the company launched a crowd funding campaign (see video below) to produce flowers that can change colors.
And what is the revolution?
“We want to change the world,” says Keira. “We really want to make a difference in the way people think about biotechnology. For a long time it’s been the realm of large companies and behind-the-scenes labs, and we want to make it a part of folks' everyday lives.”
Today we bring you a story which you probably wouldn’t have heard at last week’s AGBT conference at Marcos Island. While PacBio and 10X Genomics were getting most of the buzz at the annual show on all things sequencing, it could be the new BGI/Complete Genomics platform that steals the show later this year, says David Smith, a cancer researcher at the Mayo Clinic.
In his research, David uses sequencing to analyze the connection between the human papillomavirus (HPV) with oropharyngeall cancer.
For many years, the trend in biotech was for drug development companies to pursue one or maybe two drug candidates, or assets, as they’re called in industry parlance. Go lean and attract the attention of big pharma or investors in the late stage trials. But today’s guest says there is more innovation when the biotech organization invests in a technology platform that produces multiple drug candidates. Paul Hastings is the CEO of OncoMed, a company developing drugs that target cancer stem cells. He’s built OncoMed in what he says was the old model.
In today’s special studio interview, the health tech duo, David Shaywitz and Lisa Suennen, walk us through the changing paradigms around healthcare. They offer their thoughts on some of the new digital health and peer-to-peer social platforms which are becoming integrated in daily clinical care.
One of those attending the recent White House gathering where Obama announced the Precision Medicine Initiative was a woman who has worked tirelessly as a patient advocate for over twenty years. She’s an award winning scientist and the CEO of the Genetic Alliance: Sharon Terry joins us to kick off a new series, Personalized Medicine and the Consumerization of Healthcare.
Today we bring you a story which fits nicely in the vein of personalized medicine. But this time with a twist.
We talk with the CEO of Protagen, a company that has developed a platform to find new biomarkers for disease, particularly autoimmune diseases such as SLE, or Systemic Lupus Erythematosus. But the platform is based on the hunt for genetic mutations. Rather the company is using antibodies, or proteins to better define disease and disease populations. The company is able to stratify auto-immune diseases better than we’ve done with genomics.
This past month one of the most successful genetic testing companies, Myriad Genetics, has been settling one gene patent case after another. Also, the FDA has been attempting to regulate some very complicated lab testing. So we figured we better talk to a lawyer about the devil in the details. We’ve chosen Antoinette Konski of the law firm, Foley and Lardner.
Antoinette agrees that the Myriad settlements indicate the end of an era with gene patents. So how is she advising her life science clients in securing IP?
David Schwartz was focused on long read sequencing and the structural variations of the genome—the big picture—long before the current trend. His lab at the University of Wisconsin at Madison developed optical mapping and posted the first optical map of the human genome several years ago. And last year, they published the first optical map of a cancer genome.
Just less than a year ago, the national biotech editor at Xconomy, Luke Timmerman, left his post. Yeah, he just left it. Gone was the regular Monday column that helped us all absorb the newest trends in biotech. Gone were the lists of companies to watch out for that made sense even if we weren't up to date on Luke's sports analogies. One day the columns were here, then they were gone. Luke said he was busy with a biography of Lee Hood, the guy who brought us automated DNA sequencing. But we all knew Luke just wanted to go climb more mountains.
We’re very pleased to have Liz Mansfield of the FDA on the program to finish up our current Special Report on LDTs Series. Liz is part of the team at the FDA working on the new guidance for the regulation of LDTs, and she was at the recent meeting the FDA held to receive community feedback. Today we get into some of the details of that feedback. Did Liz and the FDA hear any new issues that they had not already considered? What about the BRAF testing that was mentioned in the meeting? Is there a risk that patients will lose access to some important tests?
Amy Miller is the Executive Vice President for the Personalized Medicine Coalition (PMC) and joins us in our Special Report on LDTs Series. Though the PMC does not have a position on whether the FDA should regulate LDTs, Amy says that the stakes could not be higher.
“We see the future of personalized medicine is at stake. We urge the FDA to get this right the first time so that personalized medicine can continue to improve the quality of care that patients currently have access to,” she says at the outset of today’s interview.
Guest:
John LaMattina, Senior Partner, Pure Tech Ventures Bio and Contact Info Listen (6:27) Comparing drug approvals: 2014 with 1996
Listen (7:10) More rational drug development?
Guest:
Paul Beresford, VP of Bus Dev, Biodesix Bio and Contact Info Listen (4:47) VeriStrat - a test for non-small cell lung cancer
Listen (4:39) What do you anticipate on the regulatory front?
Guest:
Elaine Lyon, Former President, AMP; Medical Director of Molecular Genetics, ARUP Laboratories Bio and Contact Info Listen (4:37) What is at stake here?
Listen (6:16) Is your message being heard?
Guest:
David Rimm, Professor of Pathology, Yale University School of Medicine Bio and Contact Info Listen (4:16) An unsexy science
Listen (5:36) A lack of certifications
Guest:
Anna Barker, Co-Director, Complex Adaptive Systems Center, ASU Bio and Contact Info Listen (3:21) Andy's challenge
Listen (4:39) The year of immunotherapy
Trailer for This Month in Biotech - A new monthly show from the producers of Mendelspod.
Coming January 30th.
Guest:
Surbhi Sarna, Founder, CEO, nVision Medical
Bio and Contact Info Listen (4:43) Filling a void in female health innovation
Listen (4:31) Addressing the leading cause of infertility
We perform therapeutic and diagnostic clinical trials to learn the safety and efficacy of drugs and tests in a clinical setting. Typically, we think about the biospecimens in a clinical study in terms of operational requirements such as sample collection, processing, storage and analysis. Our ability to obtain and test high quality patient samples is an important consideration during the design of clinical research programs and may significantly limit the questions that we can ask in trials.
Guest:
Carolyn Compton, Professor of Pathology, ASU Bio and Contact Info Listen (4:54) A historic new consensus
Listen (6:33) CAP committed to enforcement
Guest:
Geoffrey Ginsburg, Director, Duke Center for Applied Genomics and Precision Medicine Bio and Contact Info Listen (6:58) Genomic medicine occuring across the lifespan
Guest:
Thomas Quertermous, Director of Research, Division of Cardiovascular Medicine, Stanford University Bio and Contact Info Listen (7:45) Close, but not quite there
Guest:
Kim Stanley Robinson, Sci-Fi Author Bio and Contact Info Listen (3:30) Creating plot when science wants to be boring
Listen (3:22) Genetics and the distant past
It’s no surpise that Peter Thiel advocates for dropping out of college. Back in 2011 his extreme viewpoint garnered national media attention. Unfortunately his reasoning is no clearer today than it was three years ago. Peter lives in the Silicon Valley bubble, (or what sci-fi author, Kim Stanley Robinson, calls the Silicon Valley Fantasy Trip in today’s interview) where the final measurement for everything is financial, and it’s all about whether you got in on the next big tech company.
Guest:
Mara Aspinall, Founder, DxInsights
Bio and Contact Info Listen (2:43) DxInsights and EPEMED
Listen (3:53) Diagnostics 5.0
Guest:
Diane C. Farhi,, MD, Senior Medical Director, Quintiles Laboratories Bio and Contact Info Listen (6:37) Tracking clinical samples around the world
Listen (5:34) How to measure sample stability
Guest:
Janet, Woodcock, MD, Director, CDER, FDA
Bio and Contact Info Listen (4:41) No agency charged with better translational outcomes
Guest:
Scott Jewell, Senior Scientific Investigator and Director of Program for Biospecimen Science, Van Andel Institute Bio and Contact Info Listen (3:30) Do you see more creativity in the sample consent area?
It's a tradition at Mendelspod to bring you unique shows that go off the beaten track at the end of each year. In the past, we've brought you interviews with a science historian, a science comedian, sci-fi writers, and futurists.
We're just planning our lineup for holiday season 2014, and we want your suggestions. On the list so far are a philosopher, a popular sci-fi writer, and the former Deputy Director of the NCI.
Make your suggestions here.
Thank you, Theral & Ayanna
Guest:
Bonnie Anderson, CEO, Veracyte Bio and Contact Info Listen (5:58) What is the secret to your success?
Listen (4:30) Building the case for reimbursement
Guest: Alan Mendelson, Partner, Latham & Watkins Bio and Contact Info
Alan Mendelson, a partner at Latham & Watkins, is the first service provider--as opposed to a scientist, entrepreneur, or venture capitalist--to receive one of BayBio’s prestigious Pantheon Lifetime Achievement Awards. We talk to him a month before the awards ceremony which will be held in San Francisco on December 11th, 2014.
Guest:
Jim Vaught, Editor-in-Chief, Biopreservation and Biobanking Journal Bio and Contact Info Listen (6:50) The importance of better biosamples only recognized in the past 10 to 15 years
Guest:
Paul Davies, Principal Investigator, Center for the Convergence of Physical Science and Cancer Biology, ASU Bio and Contact Info Listen (4:05) The phone call
Listen (3:39) Too focused on a cure
Guest:
Jonathan Brody, Assoc Professor of Surgery, Thomas Jefferson University Bio and Contact Info Listen (8:17) BRCA testing being used for pancreatic cancer as well
Guest:
Ulf Gyllensten, Professor, Department of Immunology, Genetics, and Pathology, Uppsala University, Sweden Bio and Contact Info Listen (4:24) What are your goals at the National Genomics Infrastructure?
Guest:
Emanuel "Chip" Petricoin, Co-Director, CAPMM, George Mason University Bio and Contact Info Listen (4:00) Beyond the genome
Listen (5:30) Challenges to mapping the proteome
Guest:
Gene Myers , Founding Director, Systems Biology Center, Max Planck Institute Bio and Contact Info Listen (6:10) What have you been up to since the Celera days?
Guest: Aubrey de Grey, CoFounder, CSO, SENS Research Foundation Bio and Contact Info
Chapters: (Advance the marker)
0:35 First Rejuvenation Biotechnology Conference
4:50 Shackled by “short-termism”
6:00 Aging was not a topic for biologists
11:32 A serious nuisance
17:13 Smoking out the opposition
Guest:
Connor Dickie, CEO, Synbiota Bio and Contact Info Listen (5:13) Has open science really taken off in the life sciences?
Listen (4:58) #ScienceHack
Guest:
Michael Pishvaian, Assistant Professor, Georgetown University; CMO, Perthera Bio and Contact Info Listen (4:08) Untapped potential
Guest:
Comfort, Nathaniel, PhD, Author, Professor, History of Science, Technology and Medicine, Johns Hopkins University Bio and Contact Info Listen (4:20) Debate about race and genetics is really about social justice
Guest:
Eric Schadt, Professor & Chair Genetics and Genomic Sciences, Director Icahn Institute for Genomics and Multiscale Biology Bio and Contact Info Listen (5:01) Getting buy-in from a few lead doctors
Guest:
George Church, Professor of Genetics, Harvard Medical School Bio and Contact Info Listen (6:11) Church's Law
Listen (6:45) Colbert, Der Spiegel and Regenesis
Guest:
Dan Geraghty, Researcher, Fred Hutchinson Cancer Center; CEO, Scisco Genetics Bio and Contact Info Listen (4:43) Unable so far to find causal linkages in MHC region of the genome
Guest:
Shawn Baker, CSO, AllSeq Bio and Contact Info Listen (5:27) Taking the X Ten for a test drive
Listen (6:56) What is the latest price for a whole human genome sequence through Allseq?
Guest:
Mike Snyder, Director, Center for Genomics & Personalized Medicine, Stanford Bio and Contact Info Listen (5:44) Current method for figuring out transcriptomes is crazy
Guest:
Eliot Forster, Executive Chair, MedCity Bio and Contact Info Listen (2:54) Cashing in on illustrious life science tradition
Listen (2:56) Culture of collaboration strong in the UK
Guest:
David Haussler, Director, Center for Biomolecular Science and Engineering, UCSC
Bio and Contact Info Listen (8:08) Paperwork not algorithms the biggest challenge with bioinformatics
Guest:
Pearl Huang, VP, Global Head of DPAc, GSK Bio and Contact Info Listen (6:28) What is the Discovery Fast Track Challenge?
Listen (4:25) How do the reseachers benefit if they are chosen?
Guest:
George Poste, Chief Scientist, Complex Adaptive Systems; Regents’ Professor and Del E. Webb Chair in Health Innovation, ASU
Bio and Contact Info Listen (5:51) A paradigm shift to systems thinking
Guest:
Colleen Cutcliffe, CEO, Whole Biome
Bio and Contact Info Listen (2:32) Do we know enough about the microbiome yet to commercialize it?
Listen (5:58) The Complete Biome Test
Guests:
Liz Mansfield, Deputy Office Director of Personalized Medicine, OIR, FDA
Bio and Contact Info
Katie Serrano, Deputy Director of the Division of Chemistry and Toxicology, OIR, FDA
Bio and Contact Info Listen (4:08) What was submitted to Congress?
Guest: Steve Blank, Author, Entrepreneur, Educator Bio and Contact Info
Chapters: (Advance the marker)
Intro
0:59 What are you up to with the NIH?
4:39 The scientific method for entrepreneurship
8:14 Do scientists resist learning about business?
10:50 "I’m from the U.S. Government, and we need your help!"
Guest:
Brett Ryan Bonowicz, Filmmaker
Bio and Contact Info Listen (4:00) Where is the "fiction" in your science fiction?
Listen (4:47) Upcoming screenings
Guest:
Don Berry, Prof of Statistics, MD Anderson Cancer Center
Bio and Contact Info Listen (5:39) What is the goal of I-SPY trials?
Listen (8:31) Why were adaptive trials not introduced sooner?
Guest:
Pete Kissinger, Chemist, Purdue University
Bio and Contact Info Listen (4:43) Many problems in life science traced back to poor measurements
Listen (2:50) Innovation without quality
Guest: Brian Frezza, Co-Founder, Co-CEO, Emerald Therapeutics Bio and Contact Info
Chapters: (Advance the marker)
0:50 What is the Emerald Cloud Lab?
4:16 Does this impact the scientific method?
10:00 Pulling the labor, not the scientist out
14:20 Much more data detail
19:52 A chance to improve reproducibility
Guest:
Carolyn Compton, Professor of Pathology, ASU
Bio and Contact Info Listen (5:40) Quality of biomarker data limited by quality of biospecimen
Listen (5:24) Degradation of samples
Guest:
Liz Horn, PhD, Patient Advocate Bio and Contact Info Listen (8:22) What is biobanking?
Listen (4:05) Sample collection and the diagnostic odyssey
Guest:
Misha Angrist, Author, Assoc. Professor, Duke Institute for Genomic Sciences Bio and Contact Info Listen (7:03) Presidential bioethics commissions do not have a good record
Guest:
Misha Angrist, Author, Assoc. Professor, Duke Institute for Genomic Sciences Bio and Contact Info Listen (7:25) New MA in Bioethics and Science Policy
Guest: Liran Shlush, Researcher, Princess Margaret Cancer Center Bio and Contact Info Listen (4:44) Preleukemic stem cells
Listen (7:42) Implications for AML therapy and diagnosis
Guest:
Russ Altman, Dept Chair, Bioengineering, Stanford University Bio and Contact Info Listen (5:32) A bioinformatician bottleneck?
Listen (4:19) Does the engineer or coder have enough basic biology?
Guests:
Larry Goldstein, PhD, Director, UCSD Stem Cell Program
Bio and Contact Info Listen (3:16) Where are we at today with stem cell research?
Listen (5:14) One step beyond animal models
Guest:
Colleen Campbell, Assistant Director, University of Iowa - Iowa Institute for Human Genetics Bio and Contact Info Listen (2:35) How are you implementing genomic medicine?
Guest: Nathan Pearson, Senior Director of Scientific Engagement & Public Outreach, New York Genome Center Bio and Contact Info
Chapters: (Advance the marker)
0:44 Asking the "why" questions
5:55 The biological editor
11:53 Has the language of biology limited us scientifically?
Guest:
Martin Trey, COO, Integrated DNA Technologies Bio and Contact Info Listen (4:32) The oligo factory
Listen (3:30) How have you stayed relevant in the age of sequencing?
Guest:
Hank Greely, Professor of Law, Stanford Bio and Contact Info Listen (5:00) What's the best argument for FDA regulation of genetic testing?
Listen (10:50) A health exceptionalist
Guest: Mike Snyder, PhD, Director, Center for Genomics & Personalized Medicine, Stanford
Bio and Contact Info Listen (6:30) What are the important omics other than genomics?
Guest:
Steve Burrill, CEO, Burrill and Co Bio and Contact Info Listen (3:20) What is going on with capital markets?
Listen (6:48) Drug pricing an easy target but only 11% of healthcare cost
Guest:
Elaine Lyon, President, AMP; Director of Genetics Division, ARUP Bio and Contact Info Listen (5:53) How do you determine clinical validity?
Listen (5:41) Whole genome or exome?
Guest:
Sami Amr, PhD, Director of the Sequencing Core, Partners HealthCare Center for Personalized Genetic Medicine (PCPGM) Bio and Contact Info Listen (8:30) How is NGS sample prep improving in clinical applications?
Guest:
Anna Barker, Co-Director, Complex Adaptive Systems Center, ASU Bio and Contact Info Listen (7:54) Have we been overly reductionist in the study of disease?
Guest:
Anne Wojcicki, CEO, 23andMe Bio and Contact Info Listen (5:39) What was your personal reaction to the FDA letter?
Listen (5:34) What is the appropriate level of regulation?
Guests: Eric Topol, MD, Cardiologist, Genetic Researcher, and Technologist Bio and Contact Info Listen (4:55) DNA sequencing has come a long way since the Human Genome Project
Guest: C. Jimmy Lin, M.D., Ph.D, Founder of the Rare Genomics Institute (RGI) Bio and Contact Info There are an estimated 7,000 rare diseases. In the U.S., a rare disease is defined as one affecting less that 200,000 people, or 1 in 1,500 of the American population. Rare diseases are often referred to as neglected diseases because over the years they have not received the same amount of research as a common disease like cancer.
Guest:
Cliff Reid, CEO, Complete Genomics Bio and Contact Info Listen (3:55) What do you make of recent crackdown on genetic testing in China?
Listen (5:19) Self pay model better for health care
Guest:
Stefan Roever, CEO, Genia Bio and Contact Info Listen (7:34) Update on Genia technology
Listen (3:31) How will you compete with Illumina?
Guest:
Sabina Leonelli, Philosopher, University of Exeter Bio and Contact Info Listen (6:44) Not a fan of the term Big Data
Guest: Martin Reese, Co-founder, President & CSO, Omicia Bio and Contact Info
Chapters: (Advance the marker)
0:40 How did you get started in bioinformatics?
3:04 What is the biggest challenge with human genome interpretation?
8:01 Diagnosing Ogden Syndrome
13:30 What sets Omicia apart?
18:08 Who is ordering your tests?
Guest:
Dietrich Hauffe, Sr. VP, Life Sciences, QIAGEN Bio and Contact Info Listen (3:26) What is the big vision for QIAGEN?
Listen (2:26) Business already 50 percent clinical
Guest:
Noam Chomsky, Professor of Linguistics, MIT Bio and Contact Info Listen (6:34) Reductionism? Not so fast
Listen (3:10) How does a scientist come up with better questions?
Guest:
Mike Hunkapiller, CEO, Pacific Biosciences Bio and Contact Info Listen (4:58) What is the theme for 2014 at PacBio?
Listen (2:50) Are you working on a clinical sequencer?
Guest:
Shawn Baker, Chief Scientific Officer, AllSeq Bio and Contact Info Listen (3:39) #AGBT14: to tweet or not to tweet
Listen (6:23) Illumina solidifies dominance
Guest: Una Ryan, PhD, Chair, Bay Area BioEconomy Initiative Bio and Contact Info
Chapters: (Advance the marker)
1:43 Returning to childhood mission
9:14 Improving the image of big pharma
10:54 Goals of Bay Area BioEconomy Initiative
21:50 Investing in women led companies
Guest:
Simon Tate, Chief Scientific Officer, Convergence Pharmaceuticals Bio and Contact Info Listen (6:09) Sodium channel blockers and the Nav1.7 protein
Guest:
John Dupre, Professor, University of Exeter Bio and Contact Info Listen (2:19) Why should scientists think about philosophy?
Listen (8:47) Antireductionism
Guest:
Hadyn Parry, CEO, Oxitec Bio and Contact Info Listen (7:11) What is your commercialization plan?
Listen (5:32) The awesome trial at Mandacaru
Guest: Jonathan Hirsch, Founder, President, Syapse Bio and Contact Info
Chapters: (Advance the marker)
0:50 Why is Syapse the right solution?
6:12 What are you providing that hasn't already been there?
12:50 "Versioning" and preparing for FDA approval
15:44 How are you driving adoption of your service?
Guest:
Jim Greenwood, CEO of BIO Bio and Contact Info Listen (2:49) 2013 - the year the IPO window opened
Listen (6:02) What has been your primary concern this year?
Guest:
Gholson Lyon, Assist. Professor, Coldspring Harbor Bio and Contact Info Listen (3:39) Why are you a fan of 23andMe?
Listen (4:58) What about the quality?
Guest:
Sultan Meghji, Founder, Reformation Medicine Bio and Contact Info Listen (4:20) The end of technology as a specialty
Listen (4:12) Sequencing devices still a bottleneck for clinical genomics
Guest:
Mya Thomae, Founder, CEO, Myraqa Bio and Contact Info Listen (3:10) This letter more specific than in the past
Listen (2:51) What did 23andMe file with the FDA in 2012?